DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
ShellCommandRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - $(inputs.gvcf1)
- - $(inputs.gvcf2)
+ InlineJavascriptRequirement: {}
hints:
ResourceRequirement:
outputDirType: keep_output_dir
inputs:
- gvcf1:
- type: File
- gvcf2:
- type: File
+ gvcfarray: File[]
sample: string
reference:
type: File
gatheredgvcf:
type: File
outputBinding:
- glob: "*g.vcf.gz"
+ glob: "*.g.vcf.gz"
baseCommand: /gatk/gatk
arguments:
- "--java-options"
- "-Xmx8G"
- - MergeVcfs
- - prefix: "-I"
- valueFrom: $(inputs.gvcf1.basename)
- - prefix: "-I"
- valueFrom: $(inputs.gvcf2.basename)
+ - GatherVcfs
+ - shellQuote: false
+ valueFrom: >
+ ${
+ var cmd "";
+ for( var i = 0; i < inputs.gvcfarray.length; i++){
+ cmd += "\s echo " + "-I" + "\s" + inputs.gvcfsarray[i]
+ }
+ return cmd;
+ }
- prefix: "-O"
- valueFrom: $(inputs.sample)g.vcf.gz
+ valueFrom: $(inputs.sample).g.vcf.gz
ShellCommandRequirement: {}
InitialWorkDirRequirement:
listing:
- - $(inputs.gvcflist)
- $(inputs.gvcf1)
- $(inputs.gvcf2)
type: File
gvcf2:
type: File
- gvcflist:
- type: File
sample: string
reference:
type: File
gatheredgvcf:
type: File
outputBinding:
- glob: "*g.vcf.gz"
+ glob: "*.g.vcf.gz"
baseCommand: /gatk/gatk
- "--java-options"
- "-Xmx8G"
- GatherVcfs
- - prefix: "-I"
- valueFrom: $(inputs.gvcflist.basename)
+ - "-I"
+ - $(inputs.gvcf1.basename)
+ - "-I"
+ - $(inputs.gvcf2.basename)
- prefix: "-O"
- valueFrom: $(inputs.sample)g.vcf.gz
+ valueFrom: $(inputs.sample).g.vcf.gz
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
+ valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
- prefix: "-ERC"
valueFrom: "GVCF"
- prefix: "-GQB"
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+
+hints:
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+ keep_cache: 1024
+ ResourceRequirement:
+ ramMin: 5000
+ coresMin: 2
+
+inputs:
+ gvcf:
+ type: File
+ secondaryFiles:
+ - .tbi
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+ sample: string
+
+outputs:
+ genotypegvcf:
+ type: File
+ outputBinding:
+ glob: "*selected.g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx4G"
+ - SelectVariants
+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "--remove-unused-alternates"
+ valueFrom: "true"
+ - prefix: "-V"
+ valueFrom: $(inputs.gvcf)
+ - prefix: "-O"
+ valueFrom: $(inputs.sample)selected.g.vcf.gz
--- /dev/null
+#!/bin/bash
+
+xcov=$(echo "scale=4; $(samtools idxstats $1 | grep 'chrX[^_]' | cut -f 3)/$(samtools idxstats $1 | grep 'chrX[^_]' | cut -f 2)" | bc)
+echo $xcov
+ycov=$(echo "scale=4; $(samtools idxstats $1 | grep "chrY[^_]" | cut -f 3)/$(samtools idxstats $1 | grep "chrY[^_]" | cut -f 2)" | bc)
+echo $ycov
+
+rat=$(echo "scale=4; ${xcov}/${ycov}" | bc)
+
+echo $rat
--- /dev/null
+ERR1726424.gatk.g.vcf.gz
+ERR1726424.gatk.g.vcf_2.gz
+
+~
gvcf2:
class: File
- location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf_10.gz
+ location: keep:054cb90cfb20dedb862af1fdd636ad3f+297/ERR1726424_10.gatk.g.vcf.gz
--- /dev/null
+gvcf:
+ class: File
+ location: keep:3b34d300671c8dc8d1b2327f6ddab140+587/ERR1726424.g.vcf.gz
+
+reference:
+ class: File
+ location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+sample: ERR1726424