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lobSTR-workflow.cwl
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lobSTR-workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
p1:
type: File[]?
description: list of files containing the first end of paired end reads in fasta or fastq format
p2:
type: File[]?
description: list of files containing the second end of paired end reads in fasta or fastq format
output_prefix:
type: string
description: prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats
reference:
type: File
description: "lobSTR's bwa reference files"
rg-sample:
type: string
description: Use this in the read group SM tag
rg-lib:
type: string
description: Use this in the read group LB tag
strinfo:
type: File
description: File containing statistics for each STR.
noise_model:
type: File
description: File to read noise model parameters from (.stepmodel)
secondaryFiles:
- "^.stuttermodel"
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
hints:
DockerRequirement:
dockerPull: rabix/lobstr
steps:
lobSTR:
run: lobSTR-tool.cwl
in:
p1: p1
p2: p2
output_prefix: output_prefix
reference: reference
rg-sample: rg-sample
rg-lib: rg-lib
out: [bam, bam_stats]
samsort:
run: samtools-sort.cwl
in:
input: lobSTR/bam
output_name: {default: "aligned.sorted.bam" }
out: [output_file]
samindex:
run: samtools-index.cwl
in:
input: samsort/output_file
out: [bam_with_bai]
allelotype:
run: allelotype.cwl
in:
bam: samindex/bam_with_bai
reference: reference
output_prefix: output_prefix
noise_model: noise_model
strinfo: strinfo
out: [vcf, vcf_stats]