From b825be9a6707d90363ed45ee151cbaebdce3ff60 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Thu, 2 Jul 2020 17:04:01 +0000 Subject: [PATCH] Removing white spaces and commenting out schemas Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/cwl/helper/gvcf-to-vcf.cwl | 10 +++++----- WGS-processing/cwl/helper/mark-duplicates.cwl | 14 ++++++------- WGS-processing/cwl/helper/report-wf.cwl | 4 ++-- WGS-processing/cwl/helper/samtools-index.cwl | 10 +++++----- WGS-processing/cwl/helper/samtools-sort.cwl | 14 ++++++------- .../helper/scatter-gatk-wf-with-interval.cwl | 20 +++++++++---------- 6 files changed, 36 insertions(+), 36 deletions(-) diff --git a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl index 305227e..4df5fd8 100644 --- a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl +++ b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool -label: Convert GVCF to VCF +label: Convert GVCF to VCF requirements: - class: DockerRequirement @@ -39,7 +39,7 @@ outputs: arguments: - bcftools - - view + - view - prefix: "--min-ac" valueFrom: "1" - $(inputs.gvcf.path) @@ -62,6 +62,6 @@ $namespaces: s: https://schema.org/ edam: http://edamontology.org/ -$schemas: - - https://schema.org/version/latest/schema.rdf - - http://edamontology.org/EDAM_1.18.owl +#$schemas: +# - https://schema.org/version/latest/schema.rdf +# - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/mark-duplicates.cwl b/WGS-processing/cwl/helper/mark-duplicates.cwl index 42efa7e..1a39c12 100644 --- a/WGS-processing/cwl/helper/mark-duplicates.cwl +++ b/WGS-processing/cwl/helper/mark-duplicates.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool -label: Mark duplicates using GATK (Picard) +label: Mark duplicates using GATK (Picard) requirements: DockerRequirement: @@ -9,7 +9,7 @@ requirements: hints: ResourceRequirement: ramMin: 20000 - coresMin: 4 + coresMin: 4 arv:RuntimeConstraints: outputDirType: keep_output_dir SoftwareRequirement: @@ -22,7 +22,7 @@ inputs: bam: type: File format: edam:format_2572 # BAM - label: Sorted BAM + label: Sorted BAM outputs: dupbam: @@ -41,7 +41,7 @@ baseCommand: /gatk/gatk arguments: - "--java-options" - - "-Xmx8G" + - "-Xmx8G" - MarkDuplicates - prefix: "-I" valueFrom: $(inputs.bam.path) @@ -59,6 +59,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$schemas: - - https://schema.org/version/latest/schema.rdf - - http://edamontology.org/EDAM_1.18.owl +#$schemas: +# - https://schema.org/version/latest/schema.rdf +# - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl index a4c9b2f..296e199 100644 --- a/WGS-processing/cwl/helper/report-wf.cwl +++ b/WGS-processing/cwl/helper/report-wf.cwl @@ -3,7 +3,7 @@ class: Workflow label: Report generation workflow inputs: - gvcf: + gvcf: type: File format: edam:format_3016 # GVCF label: Gathered GVCF @@ -21,7 +21,7 @@ inputs: type: File format: edam:format_2331# HTML label: Header for HTML report - tailhtml: + tailhtml: type: File format: edam:format_2331 # HTML label: Footer for HTML report diff --git a/WGS-processing/cwl/helper/samtools-index.cwl b/WGS-processing/cwl/helper/samtools-index.cwl index 76b7402..ca6afc7 100644 --- a/WGS-processing/cwl/helper/samtools-index.cwl +++ b/WGS-processing/cwl/helper/samtools-index.cwl @@ -19,7 +19,7 @@ hints: version: [ "1.10" ] inputs: - bam: + bam: type: File format: edam:format_2572 # BAM label: Sorted BAM with labeled duplicates @@ -32,7 +32,7 @@ outputs: outputBinding: glob: "*bam" secondaryFiles: - - .bai + - .bai baseCommand: samtools @@ -49,6 +49,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$schemas: - - https://schema.org/version/latest/schema.rdf - - http://edamontology.org/EDAM_1.18.owl +#$schemas: +# - https://schema.org/version/latest/schema.rdf +# - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/samtools-sort.cwl b/WGS-processing/cwl/helper/samtools-sort.cwl index 672dead..fa9c0e9 100644 --- a/WGS-processing/cwl/helper/samtools-sort.cwl +++ b/WGS-processing/cwl/helper/samtools-sort.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool -label: Sort BAM +label: Sort BAM requirements: DockerRequirement: @@ -12,7 +12,7 @@ requirements: hints: arv:RuntimeConstraints: - keep_cache: 9216 + keep_cache: 9216 outputDirType: keep_output_dir SoftwareRequirement: packages: @@ -21,7 +21,7 @@ hints: version: [ "1.10" ] inputs: - bam: + bam: type: File format: edam:format_2572 # BAM label: Alignments in BAM format @@ -33,7 +33,7 @@ outputs: sortedbam: type: File format: edam:format_2572 # BAM - label: Sorted BAM + label: Sorted BAM outputBinding: glob: "*sorted.bam" @@ -58,6 +58,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$schemas: - - https://schema.org/version/latest/schema.rdf - - http://edamontology.org/EDAM_1.18.owl +#$schemas: +# - https://schema.org/version/latest/schema.rdf +# - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl index 2cf48b5..75c605b 100644 --- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: Workflow -label: Scattered variant calling workflow +label: Scattered variant calling workflow requirements: - class: SubworkflowFeatureRequirement @@ -25,7 +25,7 @@ inputs: - .sa - .fai - ^.dict - sample: + sample: type: string label: Sample Name knownsites: @@ -34,7 +34,7 @@ inputs: label: VCF of known polymorphic sites for BQSR secondaryFiles: - .tbi - scattercount: + scattercount: type: string label: Desired split for variant calling @@ -42,8 +42,8 @@ outputs: gatheredgvcf: type: File format: edam:format_3016 # GVCF - label: Gathered GVCF - secondaryFiles: + label: Gathered GVCF + secondaryFiles: - .tbi outputSource: gather-GVCFs/gatheredgvcf @@ -56,7 +56,7 @@ steps: scattercount: scattercount out: [intervalfiles] - recal-haplotypecaller: + recal-haplotypecaller: run: gatk-wf-with-interval.cwl scatter: intervallist in: @@ -73,7 +73,7 @@ steps: gvcfarray: recal-haplotypecaller/gvcf sample: sample reference: reference - out: [gatheredgvcf] + out: [gatheredgvcf] s:codeRepository: https://github.com/arvados/arvados-tutorial s:license: https://www.gnu.org/licenses/agpl-3.0.en.html @@ -82,6 +82,6 @@ $namespaces: s: https://schema.org/ edam: http://edamontology.org/ -$schemas: - - https://schema.org/version/latest/schema.rdf - - http://edamontology.org/EDAM_1.18.owl +#$schemas: +# - https://schema.org/version/latest/schema.rdf +# - http://edamontology.org/EDAM_1.18.owl -- 2.30.2