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rnaindel.cwl
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rnaindel.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: rnaindel
inputs:
bam:
type: File
secondaryFiles: .bai
inputBinding:
prefix: -b
doc: input BAM file
reference_fasta:
type: File
secondaryFiles: .fai
inputBinding:
prefix: -f
doc: reference genome FASTA file
data_dir:
type: Directory
inputBinding:
prefix: -d
doc: data directory contains databases and models
output_vcf:
type: string
inputBinding:
prefix: -o
doc: output vcf file name
input_vcf:
type: File?
inputBinding:
prefix: -c
doc: VCF file from other callers
star_mapq:
type: int
default: 255
inputBinding:
prefix: -q
doc: STAR mapping quality MAPQ for unique mappers (default=255)
process_num:
type: int?
default: 1
inputBinding:
prefix: -p
doc: number of cores (default=1)
non-somatic_panel:
type: File?
inputBinding:
prefix: -n
doc: user-defined panel of non-somatic indels in VCF format
heap_memory:
type: string?
inputBinding:
prefix: -m
doc: maximum heap space
log_dir:
type: Directory?
inputBinding:
prefix: -l
doc: directory to store log files
outputs:
outputs:
out_vcf:
type: File
outputBinding:
glob: $(inputs.output_vcf)
s:mainEntity:
class: s:SoftWareSourceCode
s:name: RNAIndel
s:url: https://github.com/stjude/RNAIndel
s:codeRepository: https://github.com/stjude/RNAIndel.git
s:author:
- class: s:Person
s:name: Kohei Hagiwara
s:email: mailto:[email protected]
s:author:
class: s:Person
s:name: Liang Ding
s:email: mailto:[email protected]
s:worksFor:
- class: s:Organization
s:name: St.Jude Children's Research Hospital
s:location: 262 Danny Thomas Place Memphis, TN 38105
s:department:
- class: s:Organization
s:name: Computational Biology
doc: |
Somatic indel discovery tool for tumor RNA-Seq data
$namespaces:
s: http://schema.org/
$schemas:
- https://schema.org/docs/schema_org_rdfa.html