From 47a54919ed0690e41cb3716dd38029d3aab9186c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:02:22 +0000 Subject: [PATCH 01/33] Use double quotes for closure around projectDir --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index c09a571c..9bfd2adc 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = '${projectDir}/tests/sra_ids_test.csv' + input = "${projectDir}/tests/sra_ids_test.csv" validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' } From 7afee7689ab0a75a8554b0a298d368b7e70419bc Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:02:40 +0000 Subject: [PATCH 02/33] Remove test data for sra_merge_samplesheet process --- conf/test_data.config | 30 ++++++++---------------------- 1 file changed, 8 insertions(+), 22 deletions(-) diff --git a/conf/test_data.config b/conf/test_data.config index 670115a8..167dff83 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -2,19 +2,7 @@ params { // Base directory for test data test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs" - merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ] - - def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/" - def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/" - def merge_samplesheet_urls = [] - def merge_mappings_urls = [] - - merge_samplesheet_ids.each { id -> - merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv" - merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv" - } - - fastq_ftp_ids = ["SRR13191702"] + fastq_ftp_ids = ["SRR13191702"] def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/" def fastq_ftp_urls = [] @@ -26,22 +14,20 @@ params { test_data { 'sarscov2'{ 'illumina' { - SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" - SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" + SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" } } 'generic' { 'config' { - ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" } } 'modules_local' { - multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" - sra_merge_samplesheet_samplesheets = merge_samplesheet_urls - sra_merge_samplesheet_mappings = merge_mappings_urls - sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" - sra_fastq_ftp = fastq_ftp_urls - sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" + multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" + sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" + sra_fastq_ftp = fastq_ftp_urls + sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" } } } From 209a7a4cc81c99e98dc4cf13c5158653d2b962a7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:03:56 +0000 Subject: [PATCH 03/33] Fix bugs with samplesheet merging from PR #238 --- workflows/sra/main.nf | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 16408496..de2d4d5d 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -118,10 +118,24 @@ workflow SRA { params.sample_mapping_fields ) - - // Combine all sample sheet/mapping paths into two files - ch_samplesheet=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'samplesheets.csv', newLine: true, keepHeader: true, storeDir:params.outdir) - ch_mappings=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'id_mappings.csv', newLine: true, keepHeader: true, storeDir:params.outdir) + // Merge samplesheets and mapping files across all samples + SRA_TO_SAMPLESHEET + .out + .samplesheet + .map { it[1] } + .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true) + .map { it.text.tokenize('\n').join('\n') } + .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet") + .set { ch_samplesheet } + + SRA_TO_SAMPLESHEET + .out + .mappings + .map { it[1] } + .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true) + .map { it.text.tokenize('\n').join('\n') } + .collectFile(name:'id_mappings.csv', storeDir: "${params.outdir}/samplesheet") + .set { ch_mappings } // // MODULE: Create a MutiQC config file with sample name mappings From ec8585c7256c41db61b52f20f7fbb89136c2222e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:07:13 +0000 Subject: [PATCH 04/33] Update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bfacdc2..8ade0c4c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,13 +10,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Special thanks to the following for their contributions to the release: - [Alexandru Mizeranschi](https://github.com/nicolae06) +- [Alexander Blaessle](https://github.com/alexblaessle) - [Sebastian Uhrig](https://github.com/suhrig) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes +- [PR #238](https://github.com/nf-core/fetchngs/pull/238) - Resolved bug when prefetching large studies ([#236](https://github.com/nf-core/fetchngs/issues/236)) - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169)) +- [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238) ### Software dependencies From da88dc6a32ef82098031ace5a8e01c056b8b5066 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:10:23 +0000 Subject: [PATCH 05/33] Fix nf-core lint until template updates are merged in --- .nf-core.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index 0e89cae9..2a36eda4 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -17,3 +17,6 @@ lint: - .gitignore - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md │ + - .github/workflows/linting.yml \ No newline at end of file From 05b993e8ca0388e5ad34030cb359e50830dc6d1c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:12:34 +0000 Subject: [PATCH 06/33] Fix prettier --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 2a36eda4..cc0541e3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -19,4 +19,4 @@ lint: - lib/NfcoreTemplate.groovy - .github/CONTRIBUTING.md - .github/PULL_REQUEST_TEMPLATE.md │ - - .github/workflows/linting.yml \ No newline at end of file + - .github/workflows/linting.yml From 8fc57d909dcd185017d8920afe38a61b9321de19 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 18:13:28 +0000 Subject: [PATCH 07/33] Fix prettier --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index cc0541e3..47379ac6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ lint: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md │ + - .github/PULL_REQUEST_TEMPLATE.md - .github/workflows/linting.yml From fb07b32552c552147686799f2b6832aca886944e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Jan 2024 19:59:54 +0000 Subject: [PATCH 08/33] Fix nf-test for sra_skip_fastq_download --- bin/multiqc_mappings_config.py | 5 +++-- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 12 +++++------- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py index 2fcdb49a..5b60f2e0 100755 --- a/bin/multiqc_mappings_config.py +++ b/bin/multiqc_mappings_config.py @@ -7,6 +7,7 @@ config = "sample_names_rename_buttons:\n" config += "\n".join([" - " + x.strip('"') for x in header]) config += "sample_names_rename:\n" + rename = [] for line in fin: - config += f" - [{', '.join(line.strip().split(','))}]\n" - fout.write(config) + rename.append(f" - [{', '.join(line.strip().split(','))}]") + fout.write(config + '\n'.join(sorted(rename)) + '\n') diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index cdb0965c..c7835acb 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,14 +20,13 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -36,16 +35,15 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:50:04.300075498" + "timestamp": "2024-01-04T19:59:06.257582" } } \ No newline at end of file From 7e5687a6b4e7c48fcc1e897cb5975bb79a390194 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 10:23:24 +0000 Subject: [PATCH 09/33] Change workDir to .nf-test --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index cb656b94..0799cb40 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,7 +3,7 @@ config { testsDir "." // nf-test directory including temporary files for each test - workDir "/tmp" + workDir ".nf-test" // location of library folder that is added automatically to the classpath libDir "lib/" From 0193bce55205fb453be5d8a22edb878591e8c64d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 10:40:57 +0000 Subject: [PATCH 10/33] Fix Black lint --- bin/multiqc_mappings_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/multiqc_mappings_config.py b/bin/multiqc_mappings_config.py index 5b60f2e0..3ffe35ec 100755 --- a/bin/multiqc_mappings_config.py +++ b/bin/multiqc_mappings_config.py @@ -10,4 +10,4 @@ rename = [] for line in fin: rename.append(f" - [{', '.join(line.strip().split(','))}]") - fout.write(config + '\n'.join(sorted(rename)) + '\n') + fout.write(config + "\n".join(sorted(rename)) + "\n") From 06cfcc8ffd54a8207ec8ecdada29f4359ef48d33 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 12:20:22 +0000 Subject: [PATCH 11/33] Update snapshots and remove dot from nf-test workDir --- nf-test.config | 2 +- workflows/sra/tests/main.nf.test.snap | 20 +++++++++---------- ...ra_custom_ena_metadata_fields.nf.test.snap | 20 +++++++++---------- .../sra_force_sratools_download.nf.test.snap | 12 +++++------ .../sra_nf_core_pipeline_atacseq.nf.test.snap | 20 +++++++++---------- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 20 +++++++++---------- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 20 +++++++++---------- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 20 +++++++++---------- 8 files changed, 60 insertions(+), 74 deletions(-) diff --git a/nf-test.config b/nf-test.config index 0799cb40..76aab204 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,7 +3,7 @@ config { testsDir "." // nf-test directory including temporary files for each test - workDir ".nf-test" + workDir "nf-test" // location of library folder that is added automatically to the classpath libDir "lib/" diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 885b7d6a..ce70041b 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:49:19.020482551" + "timestamp": "2024-01-05T11:53:53.509361" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 45e007d0..294a7951 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:36:57.154883885" + "timestamp": "2024-01-05T12:00:54.018925" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index f445296a..b2df7434 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -21,14 +21,13 @@ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,17 +36,16 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:43:16.468494798" + "timestamp": "2024-01-05T11:57:59.429567" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 3e9e7f31..687d857d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:47:56.240260295" + "timestamp": "2024-01-05T12:11:46.580901" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 8805d3ac..fc41c497 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:40:15.590249346" + "timestamp": "2024-01-05T12:14:34.129435" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 0853eef8..8a83465f 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:49:51.04235046" + "timestamp": "2024-01-05T12:19:15.913569" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index e364b3a9..1c946943 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -20,16 +20,15 @@ "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -38,18 +37,17 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-10-18T09:48:46.587502263" + "timestamp": "2024-01-05T12:06:14.563473" } } \ No newline at end of file From 1544d3fc65c99e7e296fb0f71efd13bd97a5d1b4 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 15:24:33 +0000 Subject: [PATCH 12/33] Use @adamrtalbot Docker runOptions fix to get nf-test running --- nf-test.config | 2 +- tests/nextflow.config | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 tests/nextflow.config diff --git a/nf-test.config b/nf-test.config index 76aab204..c880f88a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,7 +9,7 @@ config { libDir "lib/" // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" + configFile "tests/nextflow.config" // run all test with the defined docker profile from the main nextflow.config profile "" diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..c9ea8473 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1 @@ +docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -v $HOME:$HOME' \ No newline at end of file From e94ed03c49711ca425a93928b75c718954231a81 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 16:16:53 +0000 Subject: [PATCH 13/33] Bump nf-test version to 0.8.2 in CI tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1a5fe7f7..5c06c5ce 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.1" + NFTEST_VER: "0.8.2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 0b738edc859864c59f49590e27d653b35e22e0d3 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 16:27:20 +0000 Subject: [PATCH 14/33] Test adding docker.runOptions to pipeline nextflow.config --- nextflow.config | 2 +- nf-test.config | 2 +- tests/nextflow.config | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) delete mode 100644 tests/nextflow.config diff --git a/nextflow.config b/nextflow.config index 0f867a95..76ca8a36 100644 --- a/nextflow.config +++ b/nextflow.config @@ -114,7 +114,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + runOptions = '-u $(id -u):$(id -g) -v $HOME:$HOME' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' diff --git a/nf-test.config b/nf-test.config index c880f88a..76aab204 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,7 +9,7 @@ config { libDir "lib/" // location of an optional nextflow.config file specific for executing tests - configFile "tests/nextflow.config" + configFile "nextflow.config" // run all test with the defined docker profile from the main nextflow.config profile "" diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index c9ea8473..00000000 --- a/tests/nextflow.config +++ /dev/null @@ -1 +0,0 @@ -docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 -v $HOME:$HOME' \ No newline at end of file From 0a89ccbe93b687de06cfca9dbaebdd2cb22607b9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 16:38:33 +0000 Subject: [PATCH 15/33] Idiot...add docker in front of runOptions --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 76ca8a36..c849b9b8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -114,7 +114,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g) -v $HOME:$HOME' + docker.runOptions = '-u $(id -u):$(id -g) -v $HOME:$HOME' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' From 1f70b27de019c14ec1581f5c243a8a5756cdc1a6 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 17:10:22 +0000 Subject: [PATCH 16/33] Add sort logic to collectFile operator --- workflows/sra/main.nf | 4 ++-- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 10 +++++----- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index de2d4d5d..106041a4 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -123,7 +123,7 @@ workflow SRA { .out .samplesheet .map { it[1] } - .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true) + .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName }) .map { it.text.tokenize('\n').join('\n') } .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet") .set { ch_samplesheet } @@ -132,7 +132,7 @@ workflow SRA { .out .mappings .map { it[1] } - .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true) + .collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true, sort: { it.baseName }) .map { it.text.tokenize('\n').join('\n') } .collectFile(name:'id_mappings.csv', storeDir: "${params.outdir}/samplesheet") .set { ch_mappings } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index dd846643..c9217606 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" skip_fastq_download = true } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index c7835acb..3631113e 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -26,7 +26,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -35,7 +35,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -44,6 +44,6 @@ ] } ], - "timestamp": "2024-01-04T19:59:06.257582" + "timestamp": "2024-01-05T17:08:15.42871" } } \ No newline at end of file From 12597f1796d0c594f1f2b530b1306ea486a7b024 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 17:48:20 +0000 Subject: [PATCH 17/33] Update all workflow snapshots and use outputDir by default --- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test.snap | 10 +++++----- .../sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- .../tests/sra_custom_ena_metadata_fields.nf.test.snap | 10 +++++----- .../sra/tests/sra_force_sratools_download.nf.test | 2 +- .../sra/tests/sra_force_sratools_download.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 10 +++++----- 14 files changed, 42 insertions(+), 42 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index c8dce3c7..072c2ebb 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index ce70041b..ffdf20cc 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T11:53:53.509361" + "timestamp": "2024-01-05T17:31:06.996066" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index d4dd4141..262cedef 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "rnaseq" ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 294a7951..56c0505c 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T12:00:54.018925" + "timestamp": "2024-01-05T17:27:38.720872" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 62adb9af..453ab328 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" force_sratools_download = true } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index b2df7434..895d79b1 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -27,7 +27,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -36,7 +36,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -46,6 +46,6 @@ ] } ], - "timestamp": "2024-01-05T11:57:59.429567" + "timestamp": "2024-01-05T17:19:30.088408" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 00f545b5..3bb70fe6 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 687d857d..30de9de2 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T12:11:46.580901" + "timestamp": "2024-01-05T17:42:19.033613" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 62bd6380..a64d4348 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index fc41c497..97772a53 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T12:14:34.129435" + "timestamp": "2024-01-05T17:45:04.403125" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index c5e2865f..1befdba2 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "taxprofiler" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 8a83465f..1d882f8e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T12:19:15.913569" + "timestamp": "2024-01-05T17:47:55.191319" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 04485010..ba185097 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 1c946943..0b63f33d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" ], "2": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T12:06:14.563473" + "timestamp": "2024-01-05T17:35:26.463757" } } \ No newline at end of file From dd67624668b3ec89da299664e019235d554c208b Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 18:07:18 +0000 Subject: [PATCH 18/33] Use icdiff tool to show nf-test snapshot diff in Github Actions output --- .github/workflows/ci.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5c06c5ce..861dd018 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,6 +14,8 @@ on: env: NXF_ANSI_LOG: false NFTEST_VER: "0.8.2" + NFT_DIFF: "icdiff" + NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -88,6 +90,10 @@ jobs: run: | wget -qO- https://code.askimed.com/install/nf-test | bash sudo mv nf-test /usr/local/bin/ + + - name: Install icdiff for nf-test diff viewing + run: | + sudo apt install icdiff - name: Run nf-test run: | From b8d43bee4f8fed9876643c514e1bf834d34b697c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 5 Jan 2024 18:08:26 +0000 Subject: [PATCH 19/33] Fix prettier --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 861dd018..074b577d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -90,7 +90,7 @@ jobs: run: | wget -qO- https://code.askimed.com/install/nf-test | bash sudo mv nf-test /usr/local/bin/ - + - name: Install icdiff for nf-test diff viewing run: | sudo apt install icdiff From 300cb2e6a27fcb5e83a9c09389325ab19d0d3f99 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 6 Jan 2024 20:03:54 +0000 Subject: [PATCH 20/33] Bump nf-test version to 0.8.3 and remove Docker home mounts --- .github/workflows/ci.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 074b577d..b89823fc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.2" + NFTEST_VER: "0.8.3" NFT_DIFF: "icdiff" NFT_DIFF_ARGS: "-N --cols 200 -L expected -L observed -t" diff --git a/nextflow.config b/nextflow.config index c849b9b8..ad11a3fc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -114,7 +114,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g) -v $HOME:$HOME' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' From db9d949982f7edc64a705da5efb2445bb58cf92c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 6 Jan 2024 20:11:45 +0000 Subject: [PATCH 21/33] Add ch_ prefix to fastq_files channel --- workflows/sra/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 106041a4..d6fc8ce4 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -61,7 +61,7 @@ workflow SRA { .unique() .set { ch_sra_metadata } - fastq_files = Channel.empty() + ch_fastq_files = Channel.empty() if (!params.skip_fastq_download) { ch_sra_metadata @@ -93,7 +93,7 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - fastq_files + ch_fastq_files .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) .map { meta, fastq -> @@ -150,7 +150,7 @@ workflow SRA { } emit: - fastq = fastq_files + fastq = ch_fastq_files samplesheet = ch_samplesheet mappings = ch_mappings sample_mappings = ch_sample_mappings_yml From 44aa79c5e21375a729dd9eea427b5fda84db1fef Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 6 Jan 2024 20:34:30 +0000 Subject: [PATCH 22/33] Use --verbose parameter by default with nf-test --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b89823fc..8917a345 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -97,7 +97,7 @@ jobs: - name: Run nf-test run: | - nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + nf-test test --verbose --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml - name: Output log on failure if: failure() From 584fb2d44d7040ad62c02b2739b89c27e3b21c6c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 6 Jan 2024 20:35:30 +0000 Subject: [PATCH 23/33] Use relative path for --outdir because outputDir will be unique path --- .../sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- .../sra/tests/sra_force_sratools_download.nf.test | 2 +- .../sra/tests/sra_force_sratools_download.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 8 files changed, 12 insertions(+), 12 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 262cedef..d4dd4141 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "rnaseq" ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 453ab328..62adb9af 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" force_sratools_download = true } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 895d79b1..07cf1871 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -27,7 +27,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -36,7 +36,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -46,6 +46,6 @@ ] } ], - "timestamp": "2024-01-05T17:19:30.088408" + "timestamp": "2024-01-06T20:32:48.107479" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 3bb70fe6..00f545b5 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index a64d4348..62bd6380 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 1befdba2..c5e2865f 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "taxprofiler" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index ba185097..04485010 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index c9217606..dd846643 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" skip_fastq_download = true } } From 18a7c272f07e1c1b414c2ea3df11f51d4f01554f Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 6 Jan 2024 20:50:03 +0000 Subject: [PATCH 24/33] Update snapshots --- .../tests/sra_custom_ena_metadata_fields.nf.test.snap | 10 +++++----- .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++----- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 10 +++++----- .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 10 +++++----- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 10 +++++----- 6 files changed, 30 insertions(+), 30 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 56c0505c..ad611ee2 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T17:27:38.720872" + "timestamp": "2024-01-06T20:36:14.475733" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 30de9de2..3c616c12 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T17:42:19.033613" + "timestamp": "2024-01-06T20:45:29.760739" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 97772a53..2ad3280d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T17:45:04.403125" + "timestamp": "2024-01-06T20:47:23.837927" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 1d882f8e..031014c4 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T17:47:55.191319" + "timestamp": "2024-01-06T20:49:22.636476" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 0b63f33d..15043ffd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -28,7 +28,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2024-01-05T17:35:26.463757" + "timestamp": "2024-01-06T20:40:07.74118" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 3631113e..a402abdf 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,10 +6,10 @@ ], "1": [ - "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "2": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "3": [ [ @@ -26,7 +26,7 @@ ], "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" + "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], "sample_mappings": [ [ @@ -35,7 +35,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" + "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -44,6 +44,6 @@ ] } ], - "timestamp": "2024-01-05T17:08:15.42871" + "timestamp": "2024-01-06T20:43:31.440219" } } \ No newline at end of file From 95b30a62b2822fef37ad67dbfe47e0d3fdd84d5d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 14:13:14 +0000 Subject: [PATCH 25/33] Update snapshots and replace with explicit tests --- workflows/sra/main.nf | 9 +- workflows/sra/tests/main.nf.test.snap | 328 +++++++++++++++++- .../sra_custom_ena_metadata_fields.nf.test | 28 +- ...ra_custom_ena_metadata_fields.nf.test.snap | 120 ++++++- .../tests/sra_force_sratools_download.nf.test | 28 +- .../sra_force_sratools_download.nf.test.snap | 328 +++++++++++++++++- .../sra_nf_core_pipeline_atacseq.nf.test | 28 +- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 328 +++++++++++++++++- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 28 +- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 328 +++++++++++++++++- .../sra_nf_core_pipeline_taxprofiler.nf.test | 28 +- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 328 +++++++++++++++++- .../sra_nf_core_pipeline_viralrecon.nf.test | 28 +- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 328 +++++++++++++++++- .../sra/tests/sra_skip_fastq_download.nf.test | 28 +- .../sra_skip_fastq_download.nf.test.snap | 328 +++++++++++++++++- 16 files changed, 2517 insertions(+), 104 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index d6fc8ce4..3d487431 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -61,7 +61,6 @@ workflow SRA { .unique() .set { ch_sra_metadata } - ch_fastq_files = Channel.empty() if (!params.skip_fastq_download) { ch_sra_metadata @@ -93,8 +92,10 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - ch_fastq_files - .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) + SRA_FASTQ_FTP + .out + .fastq + .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) .map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] @@ -150,10 +151,10 @@ workflow SRA { } emit: - fastq = ch_fastq_files samplesheet = ch_samplesheet mappings = ch_mappings sample_mappings = ch_sample_mappings_yml + sra_metadata = ch_sra_metadata versions = ch_versions.unique() } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index ffdf20cc..f525d55d 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -3,29 +3,181 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86" ], - "2": [ + "1": [ "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" @@ -39,6 +191,164 @@ "samplesheet": [ "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86" ], + "sra_metadata": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +358,6 @@ ] } ], - "timestamp": "2024-01-05T17:31:06.996066" + "timestamp": "2024-01-07T13:27:35.094044" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index d4dd4141..356128c6 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -25,10 +25,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index ad611ee2..f182f555 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -3,29 +3,77 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX17709227", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "library_layout": "SINGLE", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "run_accession": "SRR21711856", + "single_end": true + }, + { + "experiment_accession": "SRX17709228", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "library_layout": "SINGLE", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "run_accession": "SRR21711855", + "single_end": true + }, + { + "experiment_accession": "SRX9315476", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_ftp": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "library_layout": "PAIRED", + "md5_1": "", + "md5_2": "", + "run_accession": "SRR12848126", + "single_end": false + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" @@ -39,6 +87,60 @@ "samplesheet": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], + "sra_metadata": [ + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX17709227", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "library_layout": "SINGLE", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "run_accession": "SRR21711856", + "single_end": true + }, + { + "experiment_accession": "SRX17709228", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "library_layout": "SINGLE", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "run_accession": "SRR21711855", + "single_end": true + }, + { + "experiment_accession": "SRX9315476", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_ftp": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "library_layout": "PAIRED", + "md5_1": "", + "md5_2": "", + "run_accession": "SRR12848126", + "single_end": false + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +150,6 @@ ] } ], - "timestamp": "2024-01-06T20:36:14.475733" + "timestamp": "2024-01-07T13:22:50.246795" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 62adb9af..3180d720 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 07cf1871..2dcf052c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -3,28 +3,180 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": 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"study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" @@ -38,6 +190,164 @@ "samplesheet": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], + "sra_metadata": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + 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true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -46,6 +356,6 @@ ] } ], - "timestamp": "2024-01-06T20:32:48.107479" + "timestamp": "2024-01-07T13:36:22.094035" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 00f545b5..1bcbbf72 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 3c616c12..5dd675d3 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -3,29 +3,181 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": 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"fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +358,6 @@ ] } ], - "timestamp": "2024-01-06T20:45:29.760739" + "timestamp": "2024-01-07T13:38:47.906835" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 62bd6380..c8be765b 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 2ad3280d..b831fe54 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -3,29 +3,181 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": 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"single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": 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"Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +358,6 @@ ] } ], - "timestamp": "2024-01-06T20:47:23.837927" + "timestamp": "2024-01-07T13:42:36.795022" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index c5e2865f..17ec98da 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 031014c4..d7463e04 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -3,29 +3,181 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" @@ -39,6 +191,164 @@ "samplesheet": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], + "sra_metadata": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +358,6 @@ ] } ], - "timestamp": "2024-01-06T20:49:22.636476" + "timestamp": "2024-01-07T13:46:25.989024" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 04485010..09f2a9d1 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 15043ffd..a8f29a95 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -3,29 +3,181 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,98a3ee9aa3bcc3b080247bccde481bbb", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" @@ -39,6 +191,164 @@ "samplesheet": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], + "sra_metadata": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "SRX9315476_SRR12848126_1.fastq.gz:md5,e4e86261d46fc31146e8809e605fd381", + "fastq_2": "SRX9315476_SRR12848126_2.fastq.gz:md5,b154211da872f5a99697097628aa3afb", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709227_SRR21711856.fastq.gz:md5,1fe5e87cc11c2af1584da9a75e49c4d2", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "SRX17709228_SRR21711855.fastq.gz:md5,3a4b64f005eba3923da57a5e61131c2a", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -48,6 +358,6 @@ ] } ], - "timestamp": "2024-01-06T20:40:07.74118" + "timestamp": "2024-01-07T13:31:16.501443" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index dd846643..363e246c 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -23,10 +23,30 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + } + + with(workflow.out.sra_metadata) { + assert get(0).get('experiment_accession') == 'ERX1234253' + assert get(1).get('experiment_accession') == 'SRX17709227' + assert get(2).get('experiment_accession') == 'SRX17709228' + assert get(3).get('experiment_accession') == 'SRX9315476' + } } } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index a402abdf..22e9fefc 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -3,27 +3,179 @@ "content": [ { "0": [ - - ], - "1": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], - "2": [ + "1": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" ], - "3": [ + "2": [ [ "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], + "3": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "", + "fastq_2": "", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "fastq": [ - ], "mappings": [ "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" @@ -37,6 +189,164 @@ "samplesheet": [ "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" ], + "sra_metadata": [ + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + }, + { + "base_count": "431758", + "experiment_accession": "SRX9315476", + "experiment_alias": "F11-N1-05", + "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "fastq_1": "", + "fastq_2": "", + "fastq_aspera": "", + "fastq_bytes": "", + "fastq_ftp": "", + "fastq_galaxy": "", + "fastq_md5": "", + "id": "SRX9315476_SRR12848126", + "instrument_model": "Illumina HiSeq 3000", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "F11-N1-05", + "library_selection": "RANDOM PCR", + "library_source": "GENOMIC", + "library_strategy": "Synthetic-Long-Read", + "md5_1": "", + "md5_2": "", + "read_count": "2954", + "run_accession": "SRR12848126", + "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", + "sample_accession": "SAMN16455283", + "sample_alias": "F11-N1-05", + "sample_description": "F11-N1-05", + "sample_title": "Longshanks_F11-N1-05", + "scientific_name": "Mus musculus domesticus", + "secondary_sample_accession": "SRS7540262", + "secondary_study_accession": "SRP287769", + "single_end": false, + "study_accession": "PRJNA670070", + "study_alias": "PRJNA670070", + "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", + "submission_accession": "SRA1145417", + "tax_id": "10092" + }, + { + "base_count": "573417800", + "experiment_accession": "SRX17709227", + "experiment_alias": "GSM6601460_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_bytes": "447377777", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", + "fastq_md5": "7cd1402155befc87be338132d1f31f64", + "id": "SRX17709227_SRR21711856", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601460", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "7cd1402155befc87be338132d1f31f64", + "md5_2": "", + "read_count": "11468356", + "run_accession": "SRR21711856", + "run_alias": "GSM6601460_r1", + "sample_accession": "SAMN31021823", + "sample_alias": "GSM6601460", + "sample_description": "sham-treated worms in day 5", + "sample_title": "sham-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239723", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + }, + { + "base_count": "677912850", + "experiment_accession": "SRX17709228", + "experiment_alias": "GSM6601461_r1", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "id": "SRX17709228_SRR21711855", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "GSM6601461", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "read_count": "13558257", + "run_accession": "SRR21711855", + "run_alias": "GSM6601461_r1", + "sample_accession": "SAMN31021822", + "sample_alias": "GSM6601461", + "sample_description": "PM2.5-treated worms in day 5", + "sample_title": "PM2.5-treated worms in day 5", + "scientific_name": "Caenorhabditis elegans", + "secondary_sample_accession": "SRS15239724", + "secondary_study_accession": "SRP399678", + "single_end": true, + "study_accession": "PRJNA884373", + "study_alias": "GSE214215", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "submission_accession": "SRA1507236", + "tax_id": "6239" + } + ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -44,6 +354,6 @@ ] } ], - "timestamp": "2024-01-06T20:43:31.440219" + "timestamp": "2024-01-07T13:51:43.062641" } } \ No newline at end of file From 7cc221dc8f8e3761f6c1c28fd0a8f0f56b8fc65d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 14:16:51 +0000 Subject: [PATCH 26/33] Fix snapshot for sra_skip_fastq_download --- workflows/sra/tests/sra_skip_fastq_download.nf.test | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 363e246c..a08c9afe 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -43,9 +43,9 @@ nextflow_workflow { with(workflow.out.sra_metadata) { assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' + assert get(1).get('experiment_accession') == 'SRX9315476' + assert get(2).get('experiment_accession') == 'SRX17709227' + assert get(3).get('experiment_accession') == 'SRX17709228' } } } From f08543d165ad646e477dbea03655bf90bf076695 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 14:26:06 +0000 Subject: [PATCH 27/33] Replace results with outputDir --- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- workflows/sra/tests/sra_force_sratools_download.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 356128c6..6f6cc260 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "rnaseq" ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 3180d720..f535223c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" force_sratools_download = true } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 1bcbbf72..af74f32c 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index c8be765b..e7367134 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 17ec98da..8d44a6a6 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "taxprofiler" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 09f2a9d1..592ac0e1 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index a08c9afe..857ee78b 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -17,7 +17,7 @@ nextflow_workflow { """ } params { - outdir = "results" + outdir = "$outputDir" skip_fastq_download = true } } From b0d4905d86d838827a59ec1a959e4888d78311c2 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 14:35:55 +0000 Subject: [PATCH 28/33] Reorder samples in first column of samplesheet and mappings --- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 4 ++-- workflows/sra/tests/sra_force_sratools_download.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 4 ++-- workflows/sra/tests/sra_skip_fastq_download.nf.test | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 6f6cc260..7ac84d16 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -29,13 +29,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index f535223c..ed72d48c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index af74f32c..7b316778 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index e7367134..53fcdc91 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 8d44a6a6..71605edf 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 592ac0e1..3678d9dc 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 857ee78b..73208ae4 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -27,13 +27,13 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"SRX17709227"', '"SRX17709228"', '"ERX1234253"', '"SRX9315476"'] + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] assert path(get(0)).text.contains('Illumina HiSeq 4000') } From b7cfca7d9f5f812a12d5084fcb956533c47b7ad4 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 15:47:19 +0000 Subject: [PATCH 29/33] Regenerate snapshots and remove metadata test --- workflows/sra/tests/main.nf.test | 21 ++++++++++++++---- workflows/sra/tests/main.nf.test.snap | 2 +- .../sra_custom_ena_metadata_fields.nf.test | 11 ++-------- ...ra_custom_ena_metadata_fields.nf.test.snap | 10 ++++----- .../tests/sra_force_sratools_download.nf.test | 7 ------ .../sra_force_sratools_download.nf.test.snap | 22 +++++++++---------- .../sra_nf_core_pipeline_atacseq.nf.test | 7 ------ .../sra_nf_core_pipeline_atacseq.nf.test.snap | 10 ++++----- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 7 ------ .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 ++++----- .../sra_nf_core_pipeline_taxprofiler.nf.test | 7 ------ ..._nf_core_pipeline_taxprofiler.nf.test.snap | 10 ++++----- .../sra_nf_core_pipeline_viralrecon.nf.test | 7 ------ ...a_nf_core_pipeline_viralrecon.nf.test.snap | 10 ++++----- .../sra/tests/sra_skip_fastq_download.nf.test | 7 ------ .../sra_skip_fastq_download.nf.test.snap | 10 ++++----- 16 files changed, 61 insertions(+), 97 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 072c2ebb..a57187b1 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -22,10 +22,23 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) + assert workflow.success + + with(workflow.out.samplesheet) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.mappings) { + assert path(get(0)).readLines().size() == 5 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] + assert path(get(0)).text.contains('Illumina HiSeq 4000') + } + + with(workflow.out.sample_mappings) { + assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5" + } } } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index f525d55d..a7b49740 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -358,6 +358,6 @@ ] } ], - "timestamp": "2024-01-07T13:27:35.094044" + "timestamp": "2024-01-07T15:01:05.175326" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 7ac84d16..008cc258 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -30,25 +30,18 @@ nextflow_workflow { with(workflow.out.samplesheet) { assert path(get(0)).readLines().size() == 5 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).text.contains('SINGLE') } with(workflow.out.mappings) { assert path(get(0)).readLines().size() == 5 assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).text.contains('SINGLE') } with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index f182f555..b508d313 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" ], "2": [ [ @@ -76,7 +76,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,7ee50def039a942e0ac8ca63292c8368" ], "sample_mappings": [ [ @@ -85,7 +85,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,7cc8031f595157c6ac13ba5067e4bcfb" ], "sra_metadata": [ { @@ -150,6 +150,6 @@ ] } ], - "timestamp": "2024-01-07T13:22:50.246795" + "timestamp": "2024-01-07T14:50:20.141785" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index ed72d48c..bfb7dfba 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 2dcf052c..b0879235 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -20,7 +20,7 @@ "experiment_accession": "ERX1234253", "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", - "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", "fastq_bytes": "18077", @@ -98,7 +98,7 @@ "experiment_accession": "SRX17709227", "experiment_alias": "GSM6601460_r1", "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz", + "fastq_1": "SRX17709227_SRR21711856_1.fastq.gz:md5,5f8db5a1966e244aad03f5bd9ca45b3d", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", "fastq_bytes": "447377777", @@ -137,7 +137,7 @@ "experiment_accession": "SRX17709228", "experiment_alias": "GSM6601461_r1", "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz", + "fastq_1": "SRX17709228_SRR21711855_1.fastq.gz:md5,bb3026b15647a3fc82a62ecb58641924", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", "fastq_bytes": "529798447", @@ -179,7 +179,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -188,7 +188,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,0f2c0516990774b5d7d76a7ddf763f55" ], "sra_metadata": [ { @@ -196,7 +196,7 @@ "experiment_accession": "ERX1234253", "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", - "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,98515d664854f1c96f55ac836fb671b9", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", "fastq_bytes": "18077", @@ -274,7 +274,7 @@ "experiment_accession": "SRX17709227", "experiment_alias": "GSM6601460_r1", "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "results/fastq/SRX17709227_SRR21711856_1.fastq.gz", + "fastq_1": "SRX17709227_SRR21711856_1.fastq.gz:md5,5f8db5a1966e244aad03f5bd9ca45b3d", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", "fastq_bytes": "447377777", @@ -313,7 +313,7 @@ "experiment_accession": "SRX17709228", "experiment_alias": "GSM6601461_r1", "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "results/fastq/SRX17709228_SRR21711855_1.fastq.gz", + "fastq_1": "SRX17709228_SRR21711855_1.fastq.gz:md5,bb3026b15647a3fc82a62ecb58641924", "fastq_2": "", "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", "fastq_bytes": "529798447", @@ -356,6 +356,6 @@ ] } ], - "timestamp": "2024-01-07T13:36:22.094035" + "timestamp": "2024-01-07T15:09:34.563421" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 7b316778..770915a3 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 5dd675d3..9d162743 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -180,7 +180,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -189,7 +189,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,8f985e9dd993b9c826ea095bd377d34a" ], "sra_metadata": [ { @@ -358,6 +358,6 @@ ] } ], - "timestamp": "2024-01-07T13:38:47.906835" + "timestamp": "2024-01-07T15:13:47.475783" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 53fcdc91..cbf42a53 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index b831fe54..93c66f55 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -180,7 +180,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -189,7 +189,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,c0f7d7b70e884c78f90630c695703d7b" ], "sra_metadata": [ { @@ -358,6 +358,6 @@ ] } ], - "timestamp": "2024-01-07T13:42:36.795022" + "timestamp": "2024-01-07T15:17:19.511222" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 71605edf..db0400c1 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index d7463e04..27e12abd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -180,7 +180,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -189,7 +189,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,fe3c7ba9e7b7debe07291d6125f9edc7" ], "sra_metadata": [ { @@ -358,6 +358,6 @@ ] } ], - "timestamp": "2024-01-07T13:46:25.989024" + "timestamp": "2024-01-07T15:21:54.519934" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 3678d9dc..e13f83b3 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX17709227' - assert get(2).get('experiment_accession') == 'SRX17709228' - assert get(3).get('experiment_accession') == 'SRX9315476' - } } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index a8f29a95..60708a54 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -180,7 +180,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -189,7 +189,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,99a3fd9fe3c7cad8184b1bbeadd89c45" ], "sra_metadata": [ { @@ -358,6 +358,6 @@ ] } ], - "timestamp": "2024-01-07T13:31:16.501443" + "timestamp": "2024-01-07T15:04:57.029889" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 73208ae4..f5805367 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -40,13 +40,6 @@ nextflow_workflow { with(workflow.out.sample_mappings) { assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" } - - with(workflow.out.sra_metadata) { - assert get(0).get('experiment_accession') == 'ERX1234253' - assert get(1).get('experiment_accession') == 'SRX9315476' - assert get(2).get('experiment_accession') == 'SRX17709227' - assert get(3).get('experiment_accession') == 'SRX17709228' - } } } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 22e9fefc..252392d7 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -3,10 +3,10 @@ "content": [ { "0": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" ], "1": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "2": [ [ @@ -178,7 +178,7 @@ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "mappings": [ - "id_mappings.csv:md5,ca34293cf91a004ea52627dd8b58a43a" + "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" ], "sample_mappings": [ [ @@ -187,7 +187,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,81856795ac19f44aeb72ae5b3042e609" + "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" ], "sra_metadata": [ { @@ -354,6 +354,6 @@ ] } ], - "timestamp": "2024-01-07T13:51:43.062641" + "timestamp": "2024-01-07T15:11:52.542678" } } \ No newline at end of file From f705af88bcb6fe2b8cda1de9a619ded8c2f0609e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 22:37:54 +0000 Subject: [PATCH 30/33] Remove all workflow snapshots --- workflows/sra/tests/main.nf.test.snap | 363 ------------------ ...ra_custom_ena_metadata_fields.nf.test.snap | 155 -------- .../sra_force_sratools_download.nf.test.snap | 361 ----------------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 363 ------------------ .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 363 ------------------ ..._nf_core_pipeline_taxprofiler.nf.test.snap | 363 ------------------ ...a_nf_core_pipeline_viralrecon.nf.test.snap | 363 ------------------ .../sra_skip_fastq_download.nf.test.snap | 359 ----------------- 8 files changed, 2690 deletions(-) delete mode 100644 workflows/sra/tests/main.nf.test.snap delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap deleted file mode 100644 index a7b49740..00000000 --- a/workflows/sra/tests/main.nf.test.snap +++ /dev/null @@ -1,363 +0,0 @@ -{ - "Parameters: default": { - "content": [ - { - "0": [ - "samplesheet.csv:md5,d252b222b8ef94670117780d43498b86" - ], - "1": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" - ], - "2": [ - [ - "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", - "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" - ] - ], - "3": [ - { - "base_count": "35658", - "experiment_accession": "ERX1234253", - "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", - "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", - "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", - "fastq_2": "", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_bytes": "18077", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_galaxy": 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"submission_accession": "SRA1507236", - "tax_id": "6239" - } - ], - "4": [ - "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ], - "mappings": [ - "id_mappings.csv:md5,f7c0bd1713fe14917b4298e252312296" - ], - "sample_mappings": [ - [ - "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", - "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" - ] - ], - "samplesheet": [ - "samplesheet.csv:md5,eb18025bb1cb97a4fe399ca16757d2db" - ], - "sra_metadata": [ - { - "base_count": "35658", - "experiment_accession": "ERX1234253", - "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", - "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_2": "", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_bytes": "18077", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", - "id": "ERX1234253_ERR1160846", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "library_layout": "SINGLE", - "library_name": "10317.BLANK.93.3E.r22", - "library_selection": "PCR", - "library_source": "METAGENOMIC", - "library_strategy": "AMPLICON", - "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", - "md5_2": "", - "read_count": "283", - "run_accession": "ERR1160846", - "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", - "sample_accession": "SAMEA3687214", - "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", - "sample_description": "American Gut control", - "sample_title": "10317.BLANK.93.3E.r22", - "scientific_name": "metagenome", - "secondary_sample_accession": "ERS994363", - "secondary_study_accession": "ERP012803", - "single_end": true, - "study_accession": "PRJEB11419", - "study_alias": "qiita_sid_10317", - "study_title": "American Gut Project", - "submission_accession": "ERA541392", - "tax_id": "256318" - }, - { - "base_count": "431758", - "experiment_accession": "SRX9315476", - "experiment_alias": "F11-N1-05", - "experiment_title": "Illumina HiSeq 3000 sequencing: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", - "fastq_1": "", - "fastq_2": "", - "fastq_aspera": "", - "fastq_bytes": "", - "fastq_ftp": "", - "fastq_galaxy": "", - "fastq_md5": "", - "id": "SRX9315476_SRR12848126", - "instrument_model": "Illumina HiSeq 3000", - "instrument_platform": "ILLUMINA", - "library_layout": "PAIRED", - "library_name": "F11-N1-05", - "library_selection": "RANDOM PCR", - "library_source": "GENOMIC", - "library_strategy": "Synthetic-Long-Read", - "md5_1": "", - "md5_2": "", - "read_count": "2954", - "run_accession": "SRR12848126", - "run_alias": "Longshanks_F11-N1-05_haplo.pMarkdup.chr3_focal.bam", - "sample_accession": "SAMN16455283", - "sample_alias": "F11-N1-05", - "sample_description": "F11-N1-05", - "sample_title": "Longshanks_F11-N1-05", - "scientific_name": "Mus musculus domesticus", - "secondary_sample_accession": "SRS7540262", - "secondary_study_accession": "SRP287769", - "single_end": false, - "study_accession": "PRJNA670070", - "study_alias": "PRJNA670070", - "study_title": "Haplotype tagging reveals parallel formation of hybrid races in two butterfly species", - "submission_accession": "SRA1145417", - "tax_id": "10092" - }, - { - "base_count": "573417800", - "experiment_accession": "SRX17709227", - "experiment_alias": "GSM6601460_r1", - "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601460: sham-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", - "fastq_2": "", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", - "fastq_bytes": "447377777", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21711856/SRR21711856.fastq.gz", - "fastq_md5": "7cd1402155befc87be338132d1f31f64", - "id": "SRX17709227_SRR21711856", - "instrument_model": "Illumina HiSeq 4000", - "instrument_platform": "ILLUMINA", - "library_layout": "SINGLE", - "library_name": "GSM6601460", - "library_selection": "cDNA", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "md5_1": "7cd1402155befc87be338132d1f31f64", - "md5_2": "", - "read_count": "11468356", - "run_accession": "SRR21711856", - "run_alias": "GSM6601460_r1", - "sample_accession": "SAMN31021823", - "sample_alias": "GSM6601460", - "sample_description": "sham-treated worms in day 5", - "sample_title": "sham-treated worms in day 5", - "scientific_name": "Caenorhabditis elegans", - "secondary_sample_accession": "SRS15239723", - "secondary_study_accession": "SRP399678", - "single_end": true, - "study_accession": "PRJNA884373", - "study_alias": "GSE214215", - "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", - "submission_accession": "SRA1507236", - "tax_id": "6239" - }, - { - "base_count": "677912850", - "experiment_accession": "SRX17709228", - "experiment_alias": "GSM6601461_r1", - "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", - "fastq_2": "", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", - "fastq_bytes": "529798447", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", - "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", - "id": "SRX17709228_SRR21711855", - "instrument_model": "Illumina HiSeq 4000", - "instrument_platform": "ILLUMINA", - "library_layout": "SINGLE", - "library_name": "GSM6601461", - "library_selection": "cDNA", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", - "md5_2": "", - "read_count": "13558257", - "run_accession": "SRR21711855", - "run_alias": "GSM6601461_r1", - "sample_accession": "SAMN31021822", - "sample_alias": "GSM6601461", - "sample_description": "PM2.5-treated worms in day 5", - "sample_title": "PM2.5-treated worms in day 5", - "scientific_name": "Caenorhabditis elegans", - "secondary_sample_accession": "SRS15239724", - "secondary_study_accession": "SRP399678", - "single_end": true, - "study_accession": "PRJNA884373", - "study_alias": "GSE214215", - "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", - "submission_accession": "SRA1507236", - "tax_id": "6239" - } - ], - "versions": [ - "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" - ] - } - ], - "timestamp": "2024-01-07T15:11:52.542678" - } -} \ No newline at end of file From 6a0120d07b5866f4674e0cf18ce650085dec5ef0 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 22:53:04 +0000 Subject: [PATCH 31/33] Tidy up tests and configuration --- conf/test.config | 4 ++-- nf-test.config | 14 ++++---------- tests/main.nf.test | 2 +- tests/nextflow.config | 0 tests/sra_ids_test.csv | 3 --- 5 files changed, 7 insertions(+), 16 deletions(-) create mode 100644 tests/nextflow.config delete mode 100644 tests/sra_ids_test.csv diff --git a/conf/test.config b/conf/test.config index 9bfd2adc..7b8941aa 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = "${projectDir}/tests/sra_ids_test.csv" + input = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv" - validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' + validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data' } diff --git a/nf-test.config b/nf-test.config index 76aab204..5721f19d 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,16 +1,10 @@ config { - // location for all nf-tests + // Location of nf-tests testsDir "." - // nf-test directory including temporary files for each test + // nf-test directory used to create temporary files for each test workDir "nf-test" - // location of library folder that is added automatically to the classpath - libDir "lib/" - - // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" - - // run all test with the defined docker profile from the main nextflow.config - profile "" + // Location of an optional nextflow.config file specific for executing pipeline tests + configFile "tests/nextflow.config" } diff --git a/tests/main.nf.test b/tests/main.nf.test index ac05aea9..6f992505 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_pipeline { max_memory = '6.GB' max_time = '6.h' input = "$projectDir/tests/sra_ids_test.csv" - validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' + validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data' } } diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..e69de29b diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv deleted file mode 100644 index d9a20c22..00000000 --- a/tests/sra_ids_test.csv +++ /dev/null @@ -1,3 +0,0 @@ -ERR1160846 -GSE214215 -SRR12848126 From f6510d596e7a7d85f75eb4cccc853ed468f2ef6b Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 22:53:35 +0000 Subject: [PATCH 32/33] Use smaller test data to speed up test runtimes --- workflows/sra/tests/main.nf.test | 16 ++++++++-------- .../tests/sra_custom_ena_metadata_fields.nf.test | 12 ++++++------ .../tests/sra_force_sratools_download.nf.test | 16 ++++++++-------- .../tests/sra_nf_core_pipeline_atacseq.nf.test | 16 ++++++++-------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 16 ++++++++-------- .../sra_nf_core_pipeline_taxprofiler.nf.test | 16 ++++++++-------- .../sra_nf_core_pipeline_viralrecon.nf.test | 16 ++++++++-------- .../sra/tests/sra_skip_fastq_download.nf.test | 16 ++++++++-------- 8 files changed, 62 insertions(+), 62 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index a57187b1..e3c3025e 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -25,19 +25,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 008cc258..b8750959 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -28,19 +28,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] assert path(get(0)).text.contains('SINGLE') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] assert path(get(0)).text.contains('SINGLE') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "3bc981f0de28023083cdf13691d249d5" + assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d" } } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index bfb7dfba..5109af7e 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 770915a3..bdd6a572 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index cbf42a53..5d8241ab 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index db0400c1..5246581e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index e13f83b3..ec57b425 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index f5805367..65a6bc28 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') + input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } params { @@ -26,19 +26,19 @@ nextflow_workflow { assert workflow.success with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 5 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"ERX1234253"', '"SRX17709227"', '"SRX17709228"', '"SRX9315476"'] - assert path(get(0)).text.contains('Illumina HiSeq 4000') + assert path(get(0)).readLines().size() == 4 + assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] + assert path(get(0)).text.contains('Illumina HiSeq 2500') } with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "6d4c3e5137704358474330207f5f2b5c" + assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" } } } From 8fc22ecef6d7463befc8036ee05a645e2810d4bd Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 7 Jan 2024 23:06:36 +0000 Subject: [PATCH 33/33] Update pipeline test to load test.config directly --- tests/main.nf.test | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/tests/main.nf.test b/tests/main.nf.test index 6f992505..f9ad32e2 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" + config "../conf/test.config" tag "pipeline" tag "pipeline_fetchngs" @@ -9,20 +10,12 @@ nextflow_pipeline { when { params { - outdir = "results" - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - input = "$projectDir/tests/sra_ids_test.csv" - validationSchemaIgnoreParams = 'test_data_base,fastq_ftp_ids,test_data' + outdir = "$outputDir" } } then { - assertAll( - { assert workflow.success } - ) + assert workflow.success } } - }