From b5666a9953955ec70dc98c0cbed0c169aea24efb Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Mon, 21 Oct 2019 14:59:12 +0100 Subject: [PATCH 1/2] Correct SevenBridges namespace --- aligner/sbg-alignment-cwl/steps/align.cwl | 2 +- aligner/sbg-alignment-cwl/steps/alignment-validation.cwl | 2 +- aligner/sbg-alignment-cwl/steps/post-align.cwl | 2 +- aligner/sbg-alignment-cwl/steps/pre-align.cwl | 2 +- aligner/sbg-alignment-cwl/steps/samtools-sort.cwl | 2 +- aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl | 2 +- aligner/sbg-alignment-cwl/topmed-alignment.cwl | 2 +- .../steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl | 2 +- .../steps/verifybamid/verifybamid.cwl | 2 +- .../topmed_freeze3_calling/topmed_freeze3_calling.cwl | 2 +- .../topmed_variant_calling_pipeline.cwl | 5 +---- .../ConcordanceTest/concordance_checker_workflow.cwl | 6 +++--- .../ConcordanceTest/gatk_concordance.cwl | 2 +- .../ConcordanceTest/gatk_concordance_checker.cwl | 2 +- .../topmed-variantcaller-checker.cwl | 2 +- .../topmed_freeze3_calling_checker.cwl | 2 +- .../sbg-variant-caller-cwl/verifybamid/verifybamid.cwl | 2 +- 17 files changed, 19 insertions(+), 22 deletions(-) diff --git a/aligner/sbg-alignment-cwl/steps/align.cwl b/aligner/sbg-alignment-cwl/steps/align.cwl index 9161a7f..11d14ba 100644 --- a/aligner/sbg-alignment-cwl/steps/align.cwl +++ b/aligner/sbg-alignment-cwl/steps/align.cwl @@ -1,7 +1,7 @@ class: CommandLineTool cwlVersion: v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' id: marko_zecevic_topmed_alignment_topmed_align_0 baseCommand: - chmod diff --git a/aligner/sbg-alignment-cwl/steps/alignment-validation.cwl b/aligner/sbg-alignment-cwl/steps/alignment-validation.cwl index f10f2b1..f209a40 100644 --- a/aligner/sbg-alignment-cwl/steps/alignment-validation.cwl +++ b/aligner/sbg-alignment-cwl/steps/alignment-validation.cwl @@ -1,7 +1,7 @@ class: CommandLineTool cwlVersion: v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' id: alignment_validation baseCommand: - '{' diff --git a/aligner/sbg-alignment-cwl/steps/post-align.cwl b/aligner/sbg-alignment-cwl/steps/post-align.cwl index 529af72..6d83da0 100644 --- a/aligner/sbg-alignment-cwl/steps/post-align.cwl +++ b/aligner/sbg-alignment-cwl/steps/post-align.cwl @@ -1,7 +1,7 @@ class: CommandLineTool cwlVersion: v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' id: marko_zecevic_topmed_alignment_topmed_post_align_3 baseCommand: - samtools diff --git a/aligner/sbg-alignment-cwl/steps/pre-align.cwl b/aligner/sbg-alignment-cwl/steps/pre-align.cwl index c301403..959a435 100644 --- a/aligner/sbg-alignment-cwl/steps/pre-align.cwl +++ b/aligner/sbg-alignment-cwl/steps/pre-align.cwl @@ -1,7 +1,7 @@ class: CommandLineTool cwlVersion: v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' id: marko_zecevic_validation_app_topmed_alignment_topmed_pre_align_7 baseCommand: - samtools diff --git a/aligner/sbg-alignment-cwl/steps/samtools-sort.cwl b/aligner/sbg-alignment-cwl/steps/samtools-sort.cwl index 77090a4..47698d3 100644 --- a/aligner/sbg-alignment-cwl/steps/samtools-sort.cwl +++ b/aligner/sbg-alignment-cwl/steps/samtools-sort.cwl @@ -1,7 +1,7 @@ class: CommandLineTool cwlVersion: v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' id: marko_zecevic_topmed_alignment_samtools_sort_0 baseCommand: - samtools diff --git a/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl b/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl index ae4594c..527abc7 100644 --- a/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl +++ b/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl @@ -4,7 +4,7 @@ id: topmed_alignment_checker doc: Checker for the TopMed alignment workflow. label: TOPMed Alignment - checker $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' inputs: - id: reference_genome 'sbg:fileTypes': 'FA, FASTA' diff --git a/aligner/sbg-alignment-cwl/topmed-alignment.cwl b/aligner/sbg-alignment-cwl/topmed-alignment.cwl index 2e3c473..1194a78 100644 --- a/aligner/sbg-alignment-cwl/topmed-alignment.cwl +++ b/aligner/sbg-alignment-cwl/topmed-alignment.cwl @@ -8,7 +8,7 @@ doc: >- Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com) label: TOPMed Alignment $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' inputs: - id: input_file 'sbg:fileTypes': CRAM diff --git a/variant-caller/sbg-variant-caller-cwl/steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl b/variant-caller/sbg-variant-caller-cwl/steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl index f92fe8e..e2d9116 100644 --- a/variant-caller/sbg-variant-caller-cwl/steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl +++ b/variant-caller/sbg-variant-caller-cwl/steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl @@ -374,4 +374,4 @@ requirements: return files.reverse(); }; $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' diff --git a/variant-caller/sbg-variant-caller-cwl/steps/verifybamid/verifybamid.cwl b/variant-caller/sbg-variant-caller-cwl/steps/verifybamid/verifybamid.cwl index 6287d5e..3fe2e0f 100755 --- a/variant-caller/sbg-variant-caller-cwl/steps/verifybamid/verifybamid.cwl +++ b/variant-caller/sbg-variant-caller-cwl/steps/verifybamid/verifybamid.cwl @@ -194,4 +194,4 @@ requirements: return files.reverse(); }; $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' diff --git a/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl b/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl index baddc22..3f5f485 100644 --- a/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl +++ b/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl @@ -541,7 +541,7 @@ hints: 'sbg:appVersion': - v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:revision': 25 'sbg:latestRevision': 25 'sbg:projectName': TOPMed Freeze 3a Variant Calling Pipeline diff --git a/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl b/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl index e06d542..01840ad 100755 --- a/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl +++ b/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl @@ -151,8 +151,5 @@ steps: requirements: - class: InlineJavascriptRequirement $namespaces: - sbg: 'https://sevenbridges.com' -'dct:creator': - 'foaf:mbox': 'mailto:vladimir.obucina@sbgenomics.com' - 'foaf:name': Vladimir Obucina + sbg: 'https://sevenbridges.com/' diff --git a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/concordance_checker_workflow.cwl b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/concordance_checker_workflow.cwl index 7faa463..b5ec35a 100644 --- a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/concordance_checker_workflow.cwl +++ b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/concordance_checker_workflow.cwl @@ -120,7 +120,7 @@ steps: https://igor.sbgenomics.com/ns/brood/images/vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/gatkconcordance/1.png 'sbg:sbgMaintained': false $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:modifiedBy': vladimir_obucina 'sbg:appVersion': - v1.0 @@ -210,7 +210,7 @@ steps: https://igor.sbgenomics.com/ns/brood/images/vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/gatkconcordancechecker/2.png 'sbg:sbgMaintained': false $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:modifiedBy': vladimir_obucina 'sbg:appVersion': - v1.0 @@ -253,7 +253,7 @@ requirements: [] 'sbg:appVersion': - v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:revision': 4 'sbg:revisionsInfo': - 'sbg:revision': 0 diff --git a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance.cwl b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance.cwl index 976e0b5..0de4f52 100644 --- a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance.cwl +++ b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance.cwl @@ -61,7 +61,7 @@ requirements: 'sbg:appVersion': - v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:revision': 1 'sbg:revisionsInfo': - 'sbg:revision': 0 diff --git a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance_checker.cwl b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance_checker.cwl index 03ba91f..a49346a 100644 --- a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance_checker.cwl +++ b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance_checker.cwl @@ -51,7 +51,7 @@ requirements: 'sbg:appVersion': - v1.0 $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:revision': 2 'sbg:revisionsInfo': - 'sbg:revision': 0 diff --git a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed-variantcaller-checker.cwl b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed-variantcaller-checker.cwl index d8217b6..7a68d85 100644 --- a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed-variantcaller-checker.cwl +++ b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed-variantcaller-checker.cwl @@ -175,4 +175,4 @@ requirements: read_and_compare_vcfs_from_tar_gz(test_vcf, truth_vcf) - class: InlineJavascriptRequirement $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' diff --git a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed_freeze3_calling_checker.cwl b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed_freeze3_calling_checker.cwl index 7cd2633..713be14 100755 --- a/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed_freeze3_calling_checker.cwl +++ b/variant-caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed_freeze3_calling_checker.cwl @@ -85,4 +85,4 @@ steps: requirements: - class: SubworkflowFeatureRequirement $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' diff --git a/variant-caller/sbg-variant-caller-cwl/verifybamid/verifybamid.cwl b/variant-caller/sbg-variant-caller-cwl/verifybamid/verifybamid.cwl index 5b171af..eb84211 100755 --- a/variant-caller/sbg-variant-caller-cwl/verifybamid/verifybamid.cwl +++ b/variant-caller/sbg-variant-caller-cwl/verifybamid/verifybamid.cwl @@ -253,7 +253,7 @@ requirements: 'sbg:modifiedBy': vladimir_obucina 'sbg:revisionNotes': 'UPDATE: GRCh37 instead of hg19' $namespaces: - sbg: 'https://sevenbridges.com' + sbg: 'https://sevenbridges.com/' 'sbg:cmdPreview': >- export PATH=$PATH:/VerifyBamID/bin/ && VerifyBamID --UDPath /VerifyBamID/resource/1000g.phase3.100k.b37.vcf.gz.dat.UD --BedPath From 4c46a709e7b986a09b9eb27ccdb0540e69e006c4 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Mon, 21 Oct 2019 15:06:19 +0100 Subject: [PATCH 2/2] Include foaf/dct namespaces --- CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl | 4 ++++ CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl | 4 ++++ aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl | 3 +++ aligner/sbg-alignment-cwl/topmed-alignment.cwl | 2 ++ aligner/topmed-cwl/workflow/alignment_workflow.cwl | 4 ++++ .../topmed_freeze3_calling/topmed_freeze3_calling.cwl | 2 ++ 6 files changed, 19 insertions(+) diff --git a/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl b/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl index 74fd736..fb8d564 100644 --- a/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl +++ b/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl @@ -1,6 +1,10 @@ cwlVersion: v1.0 class: Workflow +$namespaces: + dct: http://purl.org/dc/terms/ + foaf: http://xmlns.com/foaf/0.1/ + dct:creator: '@id': https://orcid.org/0000-0001-5173-4627 foaf:name: Walter Shands diff --git a/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl b/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl index e8e4d4c..066d2f9 100644 --- a/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl +++ b/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl @@ -1,6 +1,10 @@ cwlVersion: v1.0 class: Workflow +$namespaces: + dct: http://purl.org/dc/terms/ + foaf: http://xmlns.com/foaf/0.1/ + dct:creator: '@id': https://orcid.org/0000-0001-5173-4627 foaf:name: Walter Shands diff --git a/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl b/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl index 527abc7..5e8fe3e 100644 --- a/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl +++ b/aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl @@ -5,6 +5,9 @@ doc: Checker for the TopMed alignment workflow. label: TOPMed Alignment - checker $namespaces: sbg: 'https://sevenbridges.com/' + dct: http://purl.org/dc/terms/ + foaf: http://xmlns.com/foaf/0.1/ + inputs: - id: reference_genome 'sbg:fileTypes': 'FA, FASTA' diff --git a/aligner/sbg-alignment-cwl/topmed-alignment.cwl b/aligner/sbg-alignment-cwl/topmed-alignment.cwl index 1194a78..e68ffd9 100644 --- a/aligner/sbg-alignment-cwl/topmed-alignment.cwl +++ b/aligner/sbg-alignment-cwl/topmed-alignment.cwl @@ -9,6 +9,8 @@ doc: >- label: TOPMed Alignment $namespaces: sbg: 'https://sevenbridges.com/' + dct: http://purl.org/dc/terms/ + foaf: http://xmlns.com/foaf/0.1/ inputs: - id: input_file 'sbg:fileTypes': CRAM diff --git a/aligner/topmed-cwl/workflow/alignment_workflow.cwl b/aligner/topmed-cwl/workflow/alignment_workflow.cwl index a409c68..78194be 100644 --- a/aligner/topmed-cwl/workflow/alignment_workflow.cwl +++ b/aligner/topmed-cwl/workflow/alignment_workflow.cwl @@ -174,3 +174,7 @@ steps: reference: indexed_reference_fasta input_bam: SortBam/output_sorted_bam out: [output] + +$namespaces: + dct: http://purl.org/dc/terms/ + foaf: http://xmlns.com/foaf/0.1/ diff --git a/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl b/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl index 3f5f485..ac81f90 100644 --- a/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl +++ b/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl @@ -542,6 +542,8 @@ hints: - v1.0 $namespaces: sbg: 'https://sevenbridges.com/' + foaf: http://xmlns.com/foaf/0.1/ + dct: http://purl.org/dc/terms/ 'sbg:revision': 25 'sbg:latestRevision': 25 'sbg:projectName': TOPMed Freeze 3a Variant Calling Pipeline