outputs:
reporttxt: stdout
+ label: Annotated text from VCF
arguments:
- bcftools
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
- 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)
sample: sample
out: [bam]
samtools-sort:
- run: samtools-sort.cwl
+ run: samtools-sort.cwl
in:
bam: bwamem-samtools-view/bam
sample: sample
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
ShellCommandRequirement: {}
ResourceRequirement:
ramMin: 50000
- coresMin: 16
+ coresMin: 16
hints:
arv:RuntimeConstraints:
- keep_cache: 1024
+ keep_cache: 1024
outputDirType: keep_output_dir
SoftwareRequirement:
packages:
- .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
- $(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'
- $(inputs.fastq1)
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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
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)
outputBinding:
glob: "*fastqc.zip"
-baseCommand: fastqc
+baseCommand: fastqc
arguments:
- $(inputs.fastq1.path)
+++ /dev/null
-cwlVersion: v1.1
-class: CommandLineTool
-label: Gather GVCFs
-$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
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:
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: Gathered GVCF
+ label: Gathered GVCF
secondaryFiles:
- .tbi
outputBinding:
arguments:
- "--java-options"
- - "-Xmx8G"
+ - "-Xmx8G"
- MergeVcfs
- shellQuote: false
- valueFrom: |
+ valueFrom: |
${function compare(a, b) {
var baseA = a.basename;
var baseB = b.basename;
comparison = -1;
}
return comparison;
- }
+ }
var samples = [];
for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
- recaltable:
+ recaltable:
type: File
label: Recalibration table
intervallist:
type: File
format: edam:format_2572 # BAM
label: Recalibrated BAM for given interval
- secondaryFiles:
+ secondaryFiles:
- .bai
outputBinding:
glob: "*nodups_BQSR.bam"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
cwlVersion: v1.1
class: CommandLineTool
-label: Generate recalibration table for BQSR
+label: Generate recalibration table for BQSR
requirements:
DockerRequirement:
sample:
type: string
label: Sample Name
- knownsites:
+ knownsites:
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
- keep_cache: 1024
+ keep_cache: 1024
ResourceRequirement:
ramMin: 3500
- coresMin: 2
+ coresMin: 2
SoftwareRequirement:
packages:
GATK:
intervallist:
type: File
label: Scatter intervals file
- sample:
+ sample:
type: string
label: Sample Name
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
filteredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: Given interval filtered GVCF
+ label: Given interval filtered GVCF
outputBinding:
glob: "*g.vcf.gz"
arguments:
- "--java-options"
- "-Xmx4G"
- - SelectVariants
+ - SelectVariants
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "--remove-unused-alternates"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
- scattercount:
+ scattercount:
type: string
label: Desired split for variant calling
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl
s: https://schema.org/
edam: http://edamontology.org/
-$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