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#!/usr/bin/env cwl-runner
class: Workflow
id: test-workflow
label: test-workflow
cwlVersion: v1.0
$namespaces:
edam: 'http://edamontology.org/'
inputs:
fq1:
type: File
format: edam:format_1930
doc: FastQ file from next-generation sequencers
fq2:
type: File
format: edam:format_1930
doc: FastQ file from next-generation sequencers
ref:
type: File
format: edam:format_1929
doc: reference (e.g., hs37d5) in fasta format
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
steps:
qc1:
label: qc1
doc: Quality control for fastq file (fq1) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: fq1
out: [qc]
qc2:
label: qc2
doc: Quality control for fastq file (fq2) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: fq2
out: [qc]
trimPE:
label: trimPE
doc: adaptor trimming
run: ../Tools/trimmomaticPE.cwl
in:
fq1: fq1
fq2: fq2
out: [trimFq1P, trimFq2P]
qc1P:
label: qc1P
doc: Quality control for fastq file (fq1) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq1P
out: [qc]
qc2P:
label: qc2P
doc: Quality control for fastq file (fq2) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq2P
out: [qc]
map:
label: map
doc: Mapping onto a reference genome
run: ../Tools/bwa-mem-PE.cwl
in:
# fadir: fadir
ref: ref
fq1: trimPE/trimFq1P
fq2: trimPE/trimFq2P
out: [sam]
outputs:
oqc1:
type: File
outputSource: qc1/qc
oqc2:
type: File
outputSource: qc2/qc
oqc1P:
type: File
outputSource: qc1P/qc
oqc2P:
type: File
outputSource: qc2P/qc
sam:
type: File
outputSource: map/sam