diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md index 9c87f0a033..4d8d6bcc1b 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md @@ -1,5 +1,18 @@ # Changelog +## [0.5.4] 2025-02-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4` +- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4` + ## [0.5.3] 2024-10-01 ### Tool updates diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga index aaf2b61075..7d4ba2f241 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis on ARTIC PE data", - "release": "0.5.3", + "release": "0.5.4", "steps": { "0": { "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding", @@ -141,7 +141,7 @@ "top": 46.640625 }, "tool_id": null, - "tool_state": "{\"default\": 0.1, \"parameter_type\": \"float\", \"optional\": true}", + "tool_state": "{\"default\": 0.1, \"validators\": [], \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "29f15ec0-8fa4-4476-b649-cf68ea096744", @@ -168,7 +168,7 @@ "top": 156.640625 }, "tool_id": null, - "tool_state": "{\"default\": 1.0, \"parameter_type\": \"float\", \"optional\": true}", + "tool_state": "{\"default\": 1.0, \"validators\": [], \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "b13941c0-31c0-419d-a619-7474c24a582c", @@ -195,7 +195,7 @@ "top": 0.0 }, "tool_id": null, - "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"default\": 1, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "e33b575d-e44e-451e-a2ba-5c253fdc9e5a", @@ -222,7 +222,7 @@ "top": 117.796875 }, "tool_id": null, - "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"default\": 10, \"validators\": [], \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "07e46388-c546-4425-8702-caf5d19667c1", @@ -231,7 +231,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "errors": null, "id": 8, "input_connections": { @@ -273,15 +273,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "tool_shed_repository": { - "changeset_revision": "d60c3f704da0", + "changeset_revision": "10678d49d39e", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.4+galaxy1", + "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.24.0+galaxy4", "type": "tool", "uuid": "849d9cac-14b8-4e45-823d-5747709e8b60", "when": null, @@ -403,7 +403,7 @@ }, "11": { "annotation": "", - 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"tool_version": "0.7.17.2", + "tool_version": "0.7.18", "type": "tool", "uuid": "3b5d7080-c168-4bf7-946d-9045c0a4bc4c", "when": null, @@ -461,7 +461,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 12, "input_connections": { @@ -470,12 +470,7 @@ "output_name": "bam_output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Samtools view", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Samtools view", "outputs": [ @@ -497,15 +492,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\"], \"exclusive_filter\": [\"4\", \"8\", \"256\"], \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\"], \"exclusive_filter\": [\"4\", \"8\", \"256\"], \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"1.0\", \"seed\": null}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "2f7744df-3811-4b7f-8f1f-cf8bf0ec7a0b", "when": null, @@ -533,10 +528,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool Realign reads", - "name": "reads" - }, { "description": "runtime parameter for tool Realign reads", "name": "reference_source" @@ -586,12 +577,7 @@ "output_name": "outputsam" } }, - "inputs": [ - { - "description": "runtime parameter for tool Samtools stats", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Samtools stats", "outputs": [ @@ -607,7 +593,7 @@ "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "tool_shed_repository": { - "changeset_revision": "fed4aa48ba09", + "changeset_revision": "541082d03bef", "name": "samtools_stats", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -640,12 +626,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Insert indel qualities", - "name": "reads" - } - ], + "inputs": [], "label": null, "name": "Insert indel qualities", "outputs": [ @@ -681,7 +662,7 @@ }, "16": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "errors": null, "id": 16, "input_connections": { @@ -703,10 +684,6 @@ "description": "runtime parameter for tool ivar trim", "name": "amplicons" }, - { - "description": "runtime parameter for tool ivar trim", - "name": "input_bam" - }, { "description": "runtime parameter for tool ivar trim", "name": "primer" @@ -733,15 +710,15 @@ "output_name": "output_bam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "0893a1dbb807", + "changeset_revision": "c9ef01b1cfba", "name": "ivar_trim", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"amplicons\": {\"filter_by\": \"yes\", \"__current_case__\": 1, \"amplicon_info\": {\"__class__\": \"ConnectedValue\"}}, \"inc_primers\": true, \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"min_len\": \"1\", \"min_qual\": \"0\", \"primer\": {\"source\": \"history\", \"__current_case__\": 0, \"input_bed\": {\"__class__\": \"ConnectedValue\"}}, \"primer_pos_wiggle\": \"0\", \"trimmed_length\": {\"filter\": \"auto\", \"__current_case__\": 1}, \"window_width\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.4.2+galaxy0", + "tool_version": "1.4.3+galaxy0", "type": "tool", "uuid": "7730e635-853f-4f9f-9451-bffbe6aedd15", "when": null, @@ -755,7 +732,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3", "errors": null, "id": 17, "input_connections": { @@ -769,10 +746,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool Call variants", - "name": "reads" - }, { "description": "runtime parameter for tool Call variants", "name": "reference_source" @@ -791,15 +764,15 @@ "top": 527.5 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "4805fe3d8fda", + "changeset_revision": "b11e8e9c23bf", "name": "lofreq_call", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"call_control\": {\"set_call_options\": \"yes\", \"__current_case__\": 1, \"coverage\": {\"min_cov\": \"5\", \"max_depth\": \"1000000\"}, \"pe\": {\"use_orphan\": false}, \"bc_quals\": {\"min_bq\": \"30\", \"min_alt_bq\": \"30\", \"alt_bq\": {\"modify\": \"\", \"__current_case__\": 0}}, \"align_quals\": {\"alnqual\": {\"use_alnqual\": \"\", \"__current_case__\": 0, \"alnqual_choice\": {\"alnquals_to_use\": \"\", \"__current_case__\": 1, \"extended_baq\": true}}}, \"map_quals\": {\"min_mq\": \"20\", \"use_mq\": {\"no_mq\": \"\", \"__current_case__\": 0, \"max_mq\": \"255\"}}, \"source_qual\": {\"use_src_qual\": {\"src_qual\": \"\", \"__current_case__\": 0}}, \"joint_qual\": {\"min_jq\": \"0\", \"min_alt_jq\": \"0\", \"def_alt_jq\": \"0\"}}, \"filter_control\": {\"filter_type\": \"set_custom\", \"__current_case__\": 3, \"sig\": \"0.0005\", \"bonf\": \"0\", \"others\": false}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"regions\": {\"restrict_to_region\": \"genome\", \"__current_case__\": 0}, \"variant_types\": \"--call-indels\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.1.5+galaxy2", + "tool_version": "2.1.5+galaxy3", "type": "tool", "uuid": "422c7955-7768-4745-95db-b6882f37cd4b", "when": null, @@ -813,7 +786,7 @@ }, "18": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "errors": null, "id": 18, "input_connections": { @@ -822,12 +795,7 @@ "output_name": "output_bam" } }, - "inputs": [ - { - "description": "runtime parameter for tool QualiMap BamQC", - "name": "input1" - } - ], + "inputs": [], "label": null, "name": "QualiMap BamQC", "outputs": [ @@ -845,15 +813,15 @@ "top": 772.0 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "19ece8afbaab", + "changeset_revision": "30a201c9c310", "name": "qualimap_bamqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"duplicate_skipping\": [\"0\"], \"input1\": {\"__class__\": \"ConnectedValue\"}, \"per_base_coverage\": false, \"plot_specific\": {\"n_bins\": \"400\", \"paint_chromosome_limits\": true, \"genome_gc_distr\": null, \"homopolymer_size\": \"3\"}, \"stats_regions\": {\"region_select\": \"all\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.2d+galaxy3", + "tool_version": "2.3+galaxy0", "type": "tool", "uuid": "e2c69f7d-e6fd-4c9a-bbfd-05b70e5b2129", "when": null, @@ -889,10 +857,6 @@ { "description": "runtime parameter for tool SnpSift Filter", "name": "filter_expression" - }, - { - "description": "runtime parameter for tool SnpSift Filter", - "name": "input" } ], "label": null, @@ -947,10 +911,6 @@ { "description": "runtime parameter for tool SnpSift Filter", "name": "filter_expression" - }, - { - "description": "runtime parameter for tool SnpSift Filter", - "name": "input" } ], "label": null, @@ -997,12 +957,7 @@ "output_name": "raw_data" } }, - "inputs": [ - { - "description": "runtime parameter for tool Filter failed datasets", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Filter failed datasets", "outputs": [ @@ -1032,7 +987,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1057,18 +1012,6 @@ { "description": "runtime parameter for tool ivar removereads", "name": "amplicons" - }, - { - "description": "runtime parameter for tool ivar removereads", - "name": "input_bam" - }, - { - "description": "runtime parameter for tool ivar removereads", - "name": "input_bed" - }, - { - "description": "runtime parameter for tool ivar removereads", - "name": "variants_tsv" } ], "label": null, @@ -1084,15 +1027,15 @@ "top": 48.96875 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.4.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "69797fa273c3", + "changeset_revision": "9f4805c61d29", "name": "ivar_removereads", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"amplicons\": {\"computed\": \"no\", \"__current_case__\": 1, \"amplicon_info\": {\"__class__\": \"ConnectedValue\"}}, \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"input_bed\": {\"__class__\": \"ConnectedValue\"}, \"variants_tsv\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.4.2+galaxy0", + "tool_version": "1.4.3+galaxy0", "type": "tool", "uuid": "af7d3b75-d16c-43c7-82e4-3f1388edd22c", "when": null, @@ -1115,12 +1058,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Flatten collection", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Flatten collection", "outputs": [ @@ -1150,7 +1088,7 @@ }, "24": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3", "errors": null, "id": 24, "input_connections": { @@ -1164,10 +1102,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool Call variants", - "name": "reads" - }, { "description": "runtime parameter for tool Call variants", "name": "reference_source" @@ -1186,15 +1120,15 @@ "top": 334.296875 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3", "tool_shed_repository": { - "changeset_revision": "4805fe3d8fda", + "changeset_revision": "b11e8e9c23bf", "name": "lofreq_call", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"call_control\": {\"set_call_options\": \"yes\", \"__current_case__\": 1, \"coverage\": {\"min_cov\": \"5\", \"max_depth\": \"1000000\"}, \"pe\": {\"use_orphan\": false}, \"bc_quals\": {\"min_bq\": \"30\", \"min_alt_bq\": \"30\", \"alt_bq\": {\"modify\": \"\", \"__current_case__\": 0}}, \"align_quals\": {\"alnqual\": {\"use_alnqual\": \"\", \"__current_case__\": 0, \"alnqual_choice\": {\"alnquals_to_use\": \"\", \"__current_case__\": 1, \"extended_baq\": true}}}, \"map_quals\": {\"min_mq\": \"20\", \"use_mq\": {\"no_mq\": \"\", \"__current_case__\": 0, \"max_mq\": \"255\"}}, \"source_qual\": {\"use_src_qual\": {\"src_qual\": \"\", \"__current_case__\": 0}}, \"joint_qual\": {\"min_jq\": \"0\", \"min_alt_jq\": \"0\", \"def_alt_jq\": \"0\"}}, \"filter_control\": {\"filter_type\": \"set_custom\", \"__current_case__\": 3, \"sig\": \"0.0005\", \"bonf\": \"0\", \"others\": false}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"regions\": {\"restrict_to_region\": \"genome\", \"__current_case__\": 0}, \"variant_types\": \"--call-indels\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.1.5+galaxy2", + "tool_version": "2.1.5+galaxy3", "type": "tool", "uuid": "bef93d5b-c023-459c-888c-ac3382515322", "when": null, @@ -1208,7 +1142,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1", "errors": null, "id": 25, "input_connections": { @@ -1229,10 +1163,6 @@ "label": null, "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "plots", "type": "input" @@ -1240,6 +1170,10 @@ { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1260,15 +1194,15 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "d2aaac19f42f", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.27+galaxy1", "type": "tool", "uuid": "ee2b164f-213b-4d95-9ab7-febdf5a71085", "when": null, @@ -1287,7 +1221,7 @@ }, "26": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "errors": null, "id": 26, "input_connections": { @@ -1301,10 +1235,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool bcftools annotate", - "name": "input_file" - }, { "description": "runtime parameter for tool bcftools annotate", "name": "sec_annotate" @@ -1331,15 +1261,15 @@ "top": 689.4375 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "tool_shed_repository": { - "changeset_revision": "3f62d4939d54", + "changeset_revision": "2c372041ed8c", "name": "bcftools_annotate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"output_type\": \"v\", \"sec_annofile\": {\"columns\": \"QUAL,INFO\", \"annofile\": {\"anno_fmt\": \"vcf\", \"__current_case__\": 1, \"annotations\": {\"__class__\": \"ConnectedValue\"}}, \"mark_sites\": \"-AmpliconBias\", \"min_overlap\": \"\", \"set_id\": \"\"}, \"sec_annotate\": {\"remove\": \"\", \"rename_chrs\": {\"__class__\": \"RuntimeValue\"}, \"rename_annots\": {\"__class__\": \"RuntimeValue\"}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\", \"collapse\": null, \"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"regions_overlap\": null, \"samples\": \"\", \"invert_samples\": false, \"samples_file\": {\"__class__\": \"RuntimeValue\"}, \"invert_samples_file\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy3", + "tool_version": "1.15.1+galaxy4", "type": "tool", "uuid": "c466b7da-f50c-4093-9eb5-c014ba41c1b8", "when": null, @@ -1370,10 +1300,6 @@ { "description": "runtime parameter for tool SnpSift Filter", "name": "filter_expression" - }, - { - "description": "runtime parameter for tool SnpSift Filter", - "name": "input" } ], "label": null, @@ -1432,14 +1358,6 @@ { "description": "runtime parameter for tool VCF-VCFintersect:", "name": "reference_source" - }, - { - "description": "runtime parameter for tool VCF-VCFintersect:", - "name": "vcf_input1" - }, - { - "description": "runtime parameter for tool VCF-VCFintersect:", - "name": "vcf_input2" } ], "label": null, @@ -1477,7 +1395,7 @@ }, "29": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "errors": null, "id": 29, "input_connections": { @@ -1491,10 +1409,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool bcftools annotate", - "name": "input_file" - }, { "description": "runtime parameter for tool bcftools annotate", "name": "sec_annotate" @@ -1521,15 +1435,15 @@ "top": 656.28125 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "tool_shed_repository": { - "changeset_revision": "3f62d4939d54", + "changeset_revision": "2c372041ed8c", "name": "bcftools_annotate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"output_type\": \"v\", \"sec_annofile\": {\"columns\": \"QUAL,INFO\", \"annofile\": {\"anno_fmt\": \"vcf\", \"__current_case__\": 1, \"annotations\": {\"__class__\": \"ConnectedValue\"}}, \"mark_sites\": \"+AmpliconBias\", \"min_overlap\": \"\", \"set_id\": \"\"}, \"sec_annotate\": {\"remove\": \"\", \"rename_chrs\": {\"__class__\": \"RuntimeValue\"}, \"rename_annots\": {\"__class__\": \"RuntimeValue\"}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\", \"collapse\": null, \"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"regions_overlap\": null, \"samples\": \"\", \"invert_samples\": false, \"samples_file\": {\"__class__\": \"RuntimeValue\"}, \"invert_samples_file\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy3", + "tool_version": "1.15.1+galaxy4", "type": "tool", "uuid": "c466b7da-f50c-4093-9eb5-c014ba41c1b7", "when": null, @@ -1552,12 +1466,7 @@ "output_name": "output_file" } }, - "inputs": [ - { - "description": "runtime parameter for tool Replace Text", - "name": "infile" - } - ], + "inputs": [], "label": null, "name": "Replace Text", "outputs": [ @@ -1603,10 +1512,6 @@ } }, "inputs": [ - { - "description": "runtime parameter for tool SnpEff eff:", - "name": "input" - }, { "description": "runtime parameter for tool SnpEff eff:", "name": "intervals" @@ -1677,12 +1582,7 @@ "output_name": "snpeff_output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Lofreq filter", - "name": "invcf" - } - ], + "inputs": [], "label": null, "name": "Lofreq filter", "outputs": [ @@ -1731,4 +1631,4 @@ "covid19.galaxyproject.org" ], "uuid": "864427b0-d25a-499c-b437-f83f2d6b83f2" -} +} \ No newline at end of file