From: Sarah Wait Zaranek Date: Mon, 29 Jun 2020 21:42:02 +0000 (+0000) Subject: updating for metadata and yml to check command line cwl X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/8d016e850b2ae0ed8170d44de36ec476f2a5c836 updating for metadata and yml to check command line cwl Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- diff --git a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl index 88c78e0..22ce3f6 100644 --- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl @@ -1,10 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool -label: Germline variant calling using GATK with output gvcf - -$namespaces: - arv: "http://arvados.org/cwl#" - cwltool: "http://commonwl.org/cwltool#" +label: Call variants with GATK HaplotypeCaller requirements: DockerRequirement: @@ -17,14 +13,23 @@ hints: ResourceRequirement: ramMin: 3500 coresMin: 2 + SoftwareRequirement: + packages: + GATK: + specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ] + version: [ "4.1.7" ] inputs: bam: type: File + format: edam:format_2572 # BAM + label: Recalibrated BAM for given interval secondaryFiles: - .bai reference: type: File + format: edam:format_1929 # FASTA + label: Reference genome secondaryFiles: - .amb - .ann @@ -35,11 +40,16 @@ inputs: - ^.dict intervallist: type: File - sample: string + label: Scatter intervals file + sample: + type: string + label: Sample Name outputs: gvcf: type: File + format: edam:format_3016 # GVCF + label: GVCF for given interval secondaryFiles: - .tbi outputBinding: @@ -67,3 +77,16 @@ arguments: valueFrom: "20" - prefix: "-GQB" valueFrom: "60" + +s:codeRepository: https://github.com/arvados/arvados-tutorial +s:license: https://www.gnu.org/licenses/agpl-3.0.en.html + +$namespaces: + s: https://schema.org/ + edam: http://edamontology.org/ + arv: "http://arvados.org/cwl#" + cwltool: "http://commonwl.org/cwltool#" + +$schemas: + - https://schema.org/version/latest/schema.rdf + - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/gatk-selectvariants.cwl b/WGS-processing/cwl/helper/gatk-selectvariants.cwl index 66b5d5c..8e7031a 100644 --- a/WGS-processing/cwl/helper/gatk-selectvariants.cwl +++ b/WGS-processing/cwl/helper/gatk-selectvariants.cwl @@ -1,9 +1,6 @@ cwlVersion: v1.1 class: CommandLineTool - -$namespaces: - arv: "http://arvados.org/cwl#" - cwltool: "http://commonwl.org/cwltool#" +label: Filter unused alternates requirements: DockerRequirement: @@ -16,14 +13,23 @@ hints: ResourceRequirement: ramMin: 5000 coresMin: 2 + SoftwareRequirement: + packages: + GATK: + specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ] + version: [ "4.1.7" ] inputs: gvcf: type: File + format: edam:format_3016 # GVCF + label: GVCF for given interval secondaryFiles: - .tbi reference: type: File + format: edam:format_1929 # FASTA + label: Reference genome secondaryFiles: - .amb - .ann @@ -32,11 +38,15 @@ inputs: - .sa - .fai - ^.dict - sample: string + sample: + type: string + label: Sample Name outputs: filteredgvcf: type: File + format: edam:format_3016 # GVCF + label: Given interval filtered GVCF outputBinding: glob: "*g.vcf.gz" @@ -54,3 +64,16 @@ arguments: valueFrom: $(inputs.gvcf.path) - prefix: "-O" valueFrom: selected$(inputs.gvcf.basename) + +s:codeRepository: https://github.com/arvados/arvados-tutorial +s:license: https://www.gnu.org/licenses/agpl-3.0.en.html + +$namespaces: + s: https://schema.org/ + edam: http://edamontology.org/ + arv: "http://arvados.org/cwl#" + cwltool: "http://commonwl.org/cwltool#" + +$schemas: + - https://schema.org/version/latest/schema.rdf + - http://edamontology.org/EDAM_1.18.owl diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl index ef90209..cf815a5 100644 --- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl @@ -1,6 +1,6 @@ cwlVersion: v1.1 class: Workflow -label: Variant calling workflow for single interval +label: Variant calling workflow for given interval requirements: - class: SubworkflowFeatureRequirement @@ -41,7 +41,7 @@ outputs: gvcf: type: File format: edam:format_3016 # GVCF - label: single interval filtered GVCF + label: Given interval filtered GVCF outputSource: selectvariants/filteredgvcf steps: diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl index de8ab3f..30857f4 100644 --- a/WGS-processing/cwl/helper/report-wf.cwl +++ b/WGS-processing/cwl/helper/report-wf.cwl @@ -1,5 +1,6 @@ cwlVersion: v1.1 class: Workflow +label: Report generation workflow inputs: gvcf: 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 d740222..17bb13e 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: Variant calling workflow scattered over interval splits +label: Scattered variant calling workflow requirements: - class: SubworkflowFeatureRequirement diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl index 9c1e78a..474a5e3 100644 --- a/WGS-processing/cwl/wgs-processing-wf.cwl +++ b/WGS-processing/cwl/wgs-processing-wf.cwl @@ -40,11 +40,11 @@ inputs: label: Function used to create HTML report headhtml: type: File - format: edam:format_1964 # HTML + format: edam:format_2331# HTML label: Header for HTML report tailhtml: type: File - format: edam:format_1964 # HTML + format: edam:format_2331 # HTML label: Footer for HTML report outputs: diff --git a/WGS-processing/yml/helper/gatk-baserecalibrator.yml b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml similarity index 75% rename from WGS-processing/yml/helper/gatk-baserecalibrator.yml rename to WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml index d4b3c50..7e6b16a 100644 --- a/WGS-processing/yml/helper/gatk-baserecalibrator.yml +++ b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml @@ -12,3 +12,6 @@ knownsites1: class: File location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz +intervallist: + class: File + location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list diff --git a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml index 4909ce2..f6d4943 100644 --- a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml +++ b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml @@ -1,11 +1,15 @@ bam: class: File location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam + reference: class: File location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa + sample: ERR1726424 + scattercount: '32' + knownsites1: class: File location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz