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|
#!/usr/bin/cwl-runner
cwlVersion: v1.0
class: CommandLineTool
requirements:
- $import: envvar-global.yml
- $import: samtools-docker.yml
- class: InlineJavascriptRequirement
inputs:
compression_level:
type: int?
inputBinding:
prefix: -l
doc: |
Set compression level, from 0 (uncompressed) to 9 (best)
threads:
type: int?
inputBinding:
prefix: -@
doc: Set number of sorting and compression threads [1]
memory:
type: string?
inputBinding:
prefix: -m
doc: |
Set maximum memory per thread; suffix K/M/G recognized [768M]
input:
type: File
inputBinding:
position: 1
doc: Input bam file.
output_name:
type: string
inputBinding:
position: 2
doc: Desired output filename.
sort_by_name:
type: boolean?
inputBinding:
prefix: -n
doc: Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.
outputs:
sorted:
type: File
outputBinding:
glob: $(inputs.output_name)
baseCommand: [samtools, sort]
arguments:
- -f
$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-sort.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-sort.cwl is developed for CWL consortium
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
-@ INT Set number of sorting and compression threads [1]
Legacy usage: samtools sort [options...] <in.bam> <out.prefix>
Options:
-f Use <out.prefix> as full final filename rather than prefix
-o Write final output to stdout rather than <out.prefix>.bam
-l,m,n,@ Similar to corresponding options above
|
