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Dockstore.cwl
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Dockstore.cwl
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#!/usr/bin/env cwl-runner
class: CommandLineTool
id: "cgpmap"
label: "CGP BWA-mem mapping flow"
cwlVersion: v1.0
doc: |
Please use one of the new tools for v3+:
* [dockstore-cgpmap/cgpmap-bamOut](https://dockstore.org/containers/quay.io%2Fwtsicgp%2Fdockstore-cgpmap%2Fcgpmap-bamOut)
* [dockstore-cgpmap/cgpmap-cramOut](https://dockstore.org/containers/quay.io%2Fwtsicgp%2Fdockstore-cgpmap%2Fcgpmap-cramOut)
A Docker container for PCAP-core. See the [dockstore-cgpmap](https://github.com/cancerit/dockstore-cgpmap) website for more information.
requirements:
- $mixin: cwls/mixins/requirements.yml
hints:
- $mixin: cwls/mixins/hints.yml
inputs:
reference:
type: File
doc: "The core reference (fa, fai, dict) as tar.gz"
inputBinding:
prefix: -reference
position: 1
separate: true
bwa_idx:
type: File
doc: "The BWA indexes in tar.gz"
inputBinding:
prefix: -bwa_idx
position: 2
separate: true
sample:
type: string
doc: "Sample name to be included in output [B|CR]AM header, also used to name final file"
inputBinding:
prefix: -sample
position: 3
separate: true
bwa:
type: string?
default: ' -Y -K 100000000'
doc: "Mapping and output parameters to pass to BWA-mem, see BWA docs, default ' -Y -K 100000000'"
inputBinding:
prefix: -bwa
position: 4
separate: true
shellQuote: false
groupinfo:
type: File?
doc: "Readgroup metadata file for FASTQ inputs"
inputBinding:
prefix: -groupinfo
position: 5
separate: true
mmqc:
type: boolean
doc: "Apply mismatch QC to reads following duplicate marking."
inputBinding:
prefix: -qc
position: 6
mmqcfrac:
type: float?
default: 0.05
doc: "Mismatch fraction to set as max before failing a read [0.05]"
inputBinding:
prefix: -qcf
position: 7
separate: true
bams_in:
type:
- 'null'
- type: array
items: File
doc: "Can be BAM, CRAM, fastq (paired or interleaved), BAM/CRAM can be mixed together but not FASTQ."
inputBinding:
position: 8
outputs:
out_bam:
type: File
outputBinding:
glob: $(inputs.sample).bam
out_bai:
type: File
outputBinding:
glob: $(inputs.sample).bam.bai
out_bas:
type: File
outputBinding:
glob: $(inputs.sample).bam.bas
out_md5:
type: File
outputBinding:
glob: $(inputs.sample).bam.md5
out_met:
type: File
outputBinding:
glob: $(inputs.sample).bam.met
out_maptime:
type: File
outputBinding:
glob: $(inputs.sample).bam.maptime
baseCommand: ["/opt/wtsi-cgp/bin/ds-cgpmap.pl"]
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
$namespaces:
s: http://schema.org/
s:codeRepository: https://github.com/cancerit/dockstore-cgpmap
s:license: https://spdx.org/licenses/AGPL-3.0-only
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-5634-1539
s:email: mailto:[email protected]
s:name: Keiran Raine