/usr/share/commonwl/samtools-rmdup.cwl is in samtools 1.7-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 | #!/usr/bin/cwl-runner
cwlVersion: v1.0
class: CommandLineTool
requirements:
- $import: envvar-global.yml
- $import: samtools-docker.yml
- class: InlineJavascriptRequirement
inputs:
single_end:
type: boolean
default: false
doc: |
rmdup for SE reads
input:
type: File
inputBinding:
position: 2
doc: |
Input bam file.
output_name:
type: string
inputBinding:
position: 3
pairend_as_se:
type: boolean
default: false
doc: |
treat PE reads as SE in rmdup (force -s)
outputs:
rmdup:
type: File
outputBinding:
glob: $(inputs.output_name)
doc: File with removed duplicates
baseCommand: [samtools, rmdup]
$namespaces:
s: http://schema.org/
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
s:mainEntity:
$import: samtools-metadata.yaml
s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-rmdup.cwl
s:codeRepository: https://github.com/common-workflow-language/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:author:
class: s:Person
s:name: Andrey Kartashov
s:email: mailto:Andrey.Kartashov@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0001-9102-5681
s:worksFor:
- class: s:Organization
s:name: Cincinnati Children's Hospital Medical Center
s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
s:department:
- class: s:Organization
s:name: Barski Lab
doc: |
samtools-rmdup.cwl is developed for CWL consortium
|