/
xtea_germline_hg38.cwl
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/
xtea_germline_hg38.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.gencode)
entryname: gencode.annotation.gff3
hints:
- class: DockerRequirement
dockerPull: warbler/xtea_germline:v0.2.1
baseCommand:
- "python"
- "/usr/local/bin/gnrt_pipeline_germline_cloud_v38.py"
- "-D"
- "-o"
- "run_jobs.sh"
- "--xtea"
- "/usr/local/bin/"
- "-p"
- "."
inputs:
- id: sample
type: string
inputBinding:
prefix: -i
doc: sample name
- id: input_bam
type: File
inputBinding:
prefix: -b
secondaryFiles:
- .bai
- id: genome_tar
type: File
inputBinding:
prefix: -r
doc: genome library |
gzip archive
- id: repeats_tar
type: File
inputBinding:
prefix: -l
doc: repeats library |
gzip archive
- id: gencode
type: File
doc: gencode.annotation.gff3
- id: nthreads
type: int
default: 16
inputBinding:
prefix: -n
- id: f
type: int
default: 5907
inputBinding:
prefix: -f
- id: y
type: int
default: 7
inputBinding:
prefix: -y
doc: analysis type |
1 for LINE1, 2 for ALU, 4 for SVA
outputs:
- id: output
type: File
outputBinding:
glob: $(inputs.sample + "_*" + ".tar.gz")
doc: |
run xTea