Candidate for 2.1.1 #139

GallVp · 2024-09-19T21:55:06Z

PR checklist

Made the `hic` param pattern more flexible

Updated modules to remove Bioconda `defaults` channel

Fixed flowchart syntax to remove '\n'

… than the sequence length

Now correctly validating gff files for circular sequences

Version bump to 2.1.1

Formatted mermaid chart

github-actions · 2024-09-19T21:55:17Z

This PR is against the `main` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @GallVp,

It looks like this pull-request is has been made against the Plant-Food-Research-Open/assemblyqc main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the Plant-Food-Research-Open/assemblyqc dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2024-09-19T21:56:44Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 94f8150

+| ✅ 196 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.1.1
schema_lint - Schema $id should be https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json
Found https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File does not exist: assets/nf-core-assemblyqc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
template_strings - template_strings
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-assemblyqc_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowAssemblyqc.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.check_sequence_duplicates= true
nextflow_config - Config default value correct: params.assemblathon_stats_n_limit= 100
nextflow_config - Config default value correct: params.ncbi_fcs_adaptor_skip= true
nextflow_config - Config default value correct: params.ncbi_fcs_gx_skip= true
nextflow_config - Config default value correct: params.contamination_stops_pipeline= true
nextflow_config - Config default value correct: params.busco_skip= true
nextflow_config - Config default value correct: params.tidk_skip= true
nextflow_config - Config default value correct: params.tidk_filter_size_bp= 1000000
nextflow_config - Config default value correct: params.lai_skip= true
nextflow_config - Config default value correct: params.kraken2_skip= true
nextflow_config - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
nextflow_config - Config default value correct: params.synteny_skip= true
nextflow_config - Config default value correct: params.synteny_mummer_skip= true
nextflow_config - Config default value correct: params.synteny_plotsr_skip= true
nextflow_config - Config default value correct: params.synteny_between_input_assemblies= true
nextflow_config - Config default value correct: params.synteny_mummer_plot_type= both
nextflow_config - Config default value correct: params.synteny_mummer_max_gap= 1000000
nextflow_config - Config default value correct: params.synteny_mummer_min_bundle_size= 1000
nextflow_config - Config default value correct: params.synteny_color_by_contig= true
nextflow_config - Config default value correct: params.synteny_plotsr_seq_label= Chr
nextflow_config - Config default value correct: params.merqury_skip= true
nextflow_config - Config default value correct: params.merqury_kmer_length= 21
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 512.GB
nextflow_config - Config default value correct: params.max_time= 7.day
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/base.config and Nextflow scripts.
base_config - KRAKEN2 found in conf/base.config and Nextflow scripts.
base_config - BWA_MEM found in conf/base.config and Nextflow scripts.
base_config - SAMBLASTER found in conf/base.config and Nextflow scripts.
base_config - DNADIFF found in conf/base.config and Nextflow scripts.
base_config - MERQURY_HAPMERS found in conf/base.config and Nextflow scripts.
base_config - CREATEREPORT found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SEQKIT_RMDUP found in conf/modules.config and Nextflow scripts.
modules_config - ASSEMBLATHON_STATS found in conf/modules.config and Nextflow scripts.
modules_config - FCS_FCSADAPTOR found in conf/modules.config and Nextflow scripts.
modules_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/modules.config and Nextflow scripts.
modules_config - NCBI_FCS_GX_KRONA_PLOT found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRONA_PLOT found in conf/modules.config and Nextflow scripts.
modules_config - CIRCOS found in conf/modules.config and Nextflow scripts.
modules_config - LINEARSYNTENY found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BY_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - SORT_BY_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - TIDK_EXPLORE found in conf/modules.config and Nextflow scripts.
modules_config - TIDK_SEARCH_APRIORI found in conf/modules.config and Nextflow scripts.
modules_config - TIDK_SEARCH_APOSTERIORI found in conf/modules.config and Nextflow scripts.
modules_config - TIDK_PLOT_APRIORI found in conf/modules.config and Nextflow scripts.
modules_config - TIDK_PLOT_APOSTERIORI found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_SHORTENFASTAIDS found in conf/modules.config and Nextflow scripts.
modules_config - LTRHARVEST found in conf/modules.config and Nextflow scripts.
modules_config - LTRFINDER found in conf/modules.config and Nextflow scripts.
modules_config - LTRRETRIEVER_LTRRETRIEVER found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_RESTOREGFFIDS found in conf/modules.config and Nextflow scripts.
modules_config - LTRRETRIEVER_LAI found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - SAMBLASTER found in conf/modules.config and Nextflow scripts.
modules_config - AGP2ASSEMBLY found in conf/modules.config and Nextflow scripts.
modules_config - ASSEMBLY2BEDPE found in conf/modules.config and Nextflow scripts.
modules_config - HIC2HTML found in conf/modules.config and Nextflow scripts.
modules_config - HICQC found in conf/modules.config and Nextflow scripts.
modules_config - RUNASSEMBLYVISUALIZER found in conf/modules.config and Nextflow scripts.
modules_config - TAG_ASSEMBLY found in conf/modules.config and Nextflow scripts.
modules_config - MERQURY_MERQURY found in conf/modules.config and Nextflow scripts.
modules_config - CREATEREPORT found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-19 22:24:43

Fixed the branch protection GitHub action

GallVp added 15 commits September 19, 2024 10:36

Made the hic param pattern more flexible

9bd0117

Fixed test matrix

8ae1983

Merge pull request #131 from Plant-Food-Research-Open/fix/hic_param

4ce3fdb

Made the `hic` param pattern more flexible

Updated modules to remove Bioconda defaults channel

1ea766b

Fixed flowchart syntax

dd06148

Updated changelog

e1a10b6

Merge pull request #133 from Plant-Food-Research-Open/update/modules

512a266

Updated modules to remove Bioconda `defaults` channel

Merge branch 'dev' into fix/flowchart

ec239ee

Merge pull request #134 from Plant-Food-Research-Open/fix/flowchart

d1a7cff

Fixed flowchart syntax to remove '\n'

Now gff files for circular molecules can have end coordinates greater…

e494dda

… than the sequence length

Merge pull request #136 from Plant-Food-Research-Open/fix/gff_validation

d16decb

Now correctly validating gff files for circular sequences

Version bump to 2.1.1

36455bb

Merge pull request #137 from Plant-Food-Research-Open/bump/2.1.1

a63a7cb

Version bump to 2.1.1

Formatted mermaid chart

dd3440b

Merge pull request #138 from Plant-Food-Research-Open/format/mermaid

559ded1

Formatted mermaid chart

GallVp added 2 commits September 20, 2024 10:13

Fixed the branch protection GitHub action

18b81fb

Merge pull request #140 from Plant-Food-Research-Open/fix/branch_protect

94f8150

Fixed the branch protection GitHub action

GallVp merged commit cec2728 into main Sep 19, 2024
18 of 19 checks passed

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Candidate for 2.1.1 #139

Candidate for 2.1.1 #139

GallVp commented Sep 19, 2024

github-actions bot commented Sep 19, 2024

github-actions bot commented Sep 19, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Candidate for 2.1.1 #139

Candidate for 2.1.1 #139

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GallVp commented Sep 19, 2024

PR checklist

github-actions bot commented Sep 19, 2024

This PR is against the main branch ❌

github-actions bot commented Sep 19, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

This PR is against the `main` branch ❌

github-actions bot commented Sep 19, 2024 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️