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cwlVersion: v1.0
class: Workflow
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: rabix/lobstr
inputs:
p1:
doc: list of files containing the first end of paired end reads in fasta or fastq
format
type: File[]?
p2:
doc: list of files containing the second end of paired end reads in fasta or fastq
format
type: File[]?
output_prefix:
doc: prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats
type: string
reference:
doc: lobSTR's bwa reference files
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .rbwt
- .rpac
- .rsa
- .sa
- ${return self.basename.replace(/(.*)ref\.fasta/, "$1chromsizes.tab");}
- ${return self.basename.replace(/(.*)ref\.fasta/, "$1mergedref.bed");}
- ${return self.basename.replace(/(.*)ref\.fasta/, "$1ref_map.tab");}
rg-sample:
doc: Use this in the read group SM tag
type: string
rg-lib:
doc: Use this in the read group LB tag
type: string
strinfo:
doc: File containing statistics for each STR.
type: File
noise_model:
doc: File to read noise model parameters from (.stepmodel)
type: File
secondaryFiles:
- ^.stuttermodel
steps:
lobSTR:
run: lobSTR-tool.cwl
out:
- bam
- bam_stats
in:
p1: p1
p2: p2
output_prefix: output_prefix
reference: reference
rg-sample: rg-sample
rg-lib: rg-lib
samsort:
run: samtools-sort.cwl
out:
- output_file
in:
input: lobSTR/bam
output_name:
default: aligned.sorted.bam
samindex:
run: samtools-index.cwl
out:
- bam_with_bai
in:
input: samsort/output_file
allelotype:
run: allelotype.cwl
out:
- vcf
- vcf_stats
in:
bam: samindex/bam_with_bai
reference: reference
output_prefix: output_prefix
noise_model: noise_model
strinfo: strinfo
outputs:
bam:
type: File
outputSource: samindex/bam_with_bai
bam_stats:
type: File
outputSource: lobSTR/bam_stats
vcf:
type: File
outputSource: allelotype/vcf
vcf_stats:
type: File
outputSource: allelotype/vcf_stats
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