From: Sarah Wait Zaranek Date: Thu, 2 Jul 2020 16:19:04 +0000 (+0000) Subject: Removing white spaces and commenting schemas X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/611c455f8a94ab5dbd5c94415802b5c7fd009ffc Removing white spaces and commenting schemas Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl index 41ec58c..bb4989e 100644 --- a/WGS-processing/cwl/helper/annotate-vcf.cwl +++ b/WGS-processing/cwl/helper/annotate-vcf.cwl @@ -32,6 +32,7 @@ inputs: outputs: reporttxt: stdout + label: Annotated text from VCF arguments: - bcftools @@ -56,6 +57,6 @@ $namespaces: s: https://schema.org/ edam: http://edamontology.org/ -$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/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl index 56efe65..ee8ae4f 100644 --- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl +++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl @@ -6,11 +6,11 @@ requirements: - class: SubworkflowFeatureRequirement inputs: - fastq1: + fastq1: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R1) - fastq2: + fastq2: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R2) @@ -91,7 +91,7 @@ steps: sample: sample out: [bam] samtools-sort: - run: samtools-sort.cwl + run: samtools-sort.cwl in: bam: bwamem-samtools-view/bam sample: sample @@ -124,7 +124,7 @@ steps: reportfunc: reportfunc headhtml: headhtml tailhtml: tailhtml - out: [report] + out: [report] s:codeRepository: https://github.com/arvados/arvados-tutorial s:license: https://www.gnu.org/licenses/agpl-3.0.en.html diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl index 0ad8184..32eb5ce 100644 --- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl +++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl @@ -8,11 +8,11 @@ requirements: ShellCommandRequirement: {} ResourceRequirement: ramMin: 50000 - coresMin: 16 + coresMin: 16 hints: arv:RuntimeConstraints: - keep_cache: 1024 + keep_cache: 1024 outputDirType: keep_output_dir SoftwareRequirement: packages: @@ -36,15 +36,15 @@ inputs: - .sa - .fai - ^.dict - fastq1: + fastq1: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R1) - fastq2: + fastq2: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R2) - sample: + sample: type: string label: Sample Name @@ -66,7 +66,7 @@ arguments: - $(runtime.cores) - $(inputs.reference) - -R - - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' + - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' - -c - '250' - $(inputs.fastq1) @@ -91,6 +91,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/fastqc.cwl b/WGS-processing/cwl/helper/fastqc.cwl index fffcdad..30193a1 100644 --- a/WGS-processing/cwl/helper/fastqc.cwl +++ b/WGS-processing/cwl/helper/fastqc.cwl @@ -14,11 +14,11 @@ hints: version: [ "0.11.9" ] inputs: - fastq1: + fastq1: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R1) - fastq2: + fastq2: type: File format: edam:format_1930 # FASTQ label: One of set of pair-end FASTQs (R2) @@ -36,7 +36,7 @@ outputs: outputBinding: glob: "*fastqc.zip" -baseCommand: fastqc +baseCommand: fastqc arguments: - $(inputs.fastq1.path) diff --git a/WGS-processing/cwl/helper/gather-array-vcf.cwl b/WGS-processing/cwl/helper/gather-array-vcf.cwl deleted file mode 100644 index 9daf557..0000000 --- a/WGS-processing/cwl/helper/gather-array-vcf.cwl +++ /dev/null @@ -1,85 +0,0 @@ -cwlVersion: v1.1 -class: CommandLineTool -label: Gather GVCFs -$namespaces: - arv: "http://arvados.org/cwl#" - cwltool: "http://commonwl.org/cwltool#" - -requirements: - DockerRequirement: - dockerPull: broadinstitute/gatk:4.1.7.0 - ShellCommandRequirement: {} - InlineJavascriptRequirement: {} - -hints: - ResourceRequirement: - ramMin: 20000 - coresMin: 4 - arv:RuntimeConstraints: - outputDirType: keep_output_dir - -inputs: - gvcfarray: - type: File[] - sample: string - reference: - type: File - secondaryFiles: - - .amb - - .ann - - .bwt - - .pac - - .sa - - .fai - - ^.dict -outputs: - gatheredgvcf: - type: File - secondaryFiles: - - .tbi - outputBinding: - glob: "*.g.vcf.gz" - -baseCommand: /gatk/gatk - -arguments: - - "--java-options" - - "-Xmx8G" - - MergeVcfs - - shellQuote: false - valueFrom: | - ${function compare(a, b) { - var baseA = a.basename; - var baseB = b.basename; - - var comparison = 0; - if (baseA > baseB) { - comparison = 1; - } else if (baseA < baseB) { - comparison = -1; - } - return comparison; - } - - var sortedarray = []; - sortedarray = inputs.gvcfarray.sort(compare) - - var samples = []; - for (var i = 0; i < sortedarray.length; i++) { - var name = sortedarray[i]; - if (name.nameext ==='.gz' ) { - samples.push(name.path); - } - } - - var sampleinput = ""; - - for (var i = 0; i < samples.length; i++) { - var s1 = samples[i]; - sampleinput = sampleinput + "-I " + s1 + " " - } - - return sampleinput; - } - - prefix: "-O" - valueFrom: $(inputs.sample).g.vcf.gz diff --git a/WGS-processing/cwl/helper/gather-vcf.cwl b/WGS-processing/cwl/helper/gather-vcf.cwl index 15b6551..b59fc35 100644 --- a/WGS-processing/cwl/helper/gather-vcf.cwl +++ b/WGS-processing/cwl/helper/gather-vcf.cwl @@ -15,16 +15,16 @@ requirements: hints: ResourceRequirement: ramMin: 20000 - coresMin: 4 + coresMin: 4 arv:RuntimeConstraints: outputDirType: keep_output_dir inputs: - gvcfdir: + gvcfdir: type: Directory label: Input directory of GVCFs loadListing: 'shallow_listing' - sample: + sample: type: string label: Sample Name reference: @@ -43,7 +43,7 @@ outputs: gatheredgvcf: type: File format: edam:format_3016 # GVCF - label: Gathered GVCF + label: Gathered GVCF secondaryFiles: - .tbi outputBinding: @@ -53,10 +53,10 @@ baseCommand: /gatk/gatk arguments: - "--java-options" - - "-Xmx8G" + - "-Xmx8G" - MergeVcfs - shellQuote: false - valueFrom: | + valueFrom: | ${function compare(a, b) { var baseA = a.basename; var baseB = b.basename; @@ -68,7 +68,7 @@ arguments: comparison = -1; } return comparison; - } + } var samples = []; for (var i = 0; i < inputs.gvcfdir.listing.length; i++) { @@ -99,6 +99,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl index f9c0fe3..d8f6afd 100644 --- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl @@ -41,10 +41,10 @@ inputs: - .sa - .fai - ^.dict - sample: + sample: type: string label: Sample Name - recaltable: + recaltable: type: File label: Recalibration table intervallist: @@ -56,7 +56,7 @@ outputs: type: File format: edam:format_2572 # BAM label: Recalibrated BAM for given interval - secondaryFiles: + secondaryFiles: - .bai outputBinding: glob: "*nodups_BQSR.bam" @@ -87,6 +87,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl index 6df9de1..80859e6 100644 --- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool -label: Generate recalibration table for BQSR +label: Generate recalibration table for BQSR requirements: DockerRequirement: @@ -44,7 +44,7 @@ inputs: sample: type: string label: Sample Name - knownsites: + knownsites: type: File format: edam:format_3016 # VCF label: VCF of known polymorphic sites for BQSR @@ -87,6 +87,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl index 22ce3f6..53d7ee2 100644 --- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl @@ -9,10 +9,10 @@ requirements: hints: arv:RuntimeConstraints: outputDirType: keep_output_dir - keep_cache: 1024 + keep_cache: 1024 ResourceRequirement: ramMin: 3500 - coresMin: 2 + coresMin: 2 SoftwareRequirement: packages: GATK: @@ -41,7 +41,7 @@ inputs: intervallist: type: File label: Scatter intervals file - sample: + sample: type: string label: Sample Name @@ -87,6 +87,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/gatk-selectvariants.cwl b/WGS-processing/cwl/helper/gatk-selectvariants.cwl index 8e7031a..bb5643b 100644 --- a/WGS-processing/cwl/helper/gatk-selectvariants.cwl +++ b/WGS-processing/cwl/helper/gatk-selectvariants.cwl @@ -38,7 +38,7 @@ inputs: - .sa - .fai - ^.dict - sample: + sample: type: string label: Sample Name @@ -46,7 +46,7 @@ outputs: filteredgvcf: type: File format: edam:format_3016 # GVCF - label: Given interval filtered GVCF + label: Given interval filtered GVCF outputBinding: glob: "*g.vcf.gz" @@ -55,7 +55,7 @@ baseCommand: /gatk/gatk arguments: - "--java-options" - "-Xmx4G" - - SelectVariants + - SelectVariants - prefix: "-R" valueFrom: $(inputs.reference) - prefix: "--remove-unused-alternates" @@ -74,6 +74,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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/gatk-splitintervals.cwl b/WGS-processing/cwl/helper/gatk-splitintervals.cwl index 9e26447..98758d1 100644 --- a/WGS-processing/cwl/helper/gatk-splitintervals.cwl +++ b/WGS-processing/cwl/helper/gatk-splitintervals.cwl @@ -32,10 +32,10 @@ inputs: - .sa - .fai - ^.dict - sample: + sample: type: string label: Sample Name - scattercount: + scattercount: type: string label: Desired split for variant calling @@ -70,6 +70,6 @@ $namespaces: arv: "http://arvados.org/cwl#" cwltool: "http://commonwl.org/cwltool#" -$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 b53f385..a4c9b2f 100644 --- a/WGS-processing/cwl/helper/report-wf.cwl +++ b/WGS-processing/cwl/helper/report-wf.cwl @@ -63,6 +63,6 @@ $namespaces: s: https://schema.org/ edam: http://edamontology.org/ -$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