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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:
sra_run_ids:
type: string[]
doc: A list of SRA Run ID such as ERR034597
download_repo:
type: string?
doc: (optional) The repository from which the data was downloaded (ncbi/ebi/ddbj). Default value is NCBI.
nthreads:
type: int
doc: The number of cores to be used for parallel exec of fastq-dump
fadir:
type: Directory
doc: directory containing FastA file and index for BWA aligner
ref:
type: string
doc: name of reference (e.g., hs37d5) for BWA aligner
steps:
download_sra:
label: download_sra
doc: Download .sra format sequence data from NCBI Sequence Read Archive
run: ../Tools/download-sra.cwl
in:
repo: download_repo
run_ids: sra_run_ids
out:
[sraFiles]
pfastq_dump:
label: pfastq-dump
doc: parallel execution of fastq-dump to convert .sra to .fastq.gz
run: ../Tools/pfastq-dump.cwl
in:
sraFiles: download_sra/sraFiles
nthreads: nthreads
out:
[forward, reverse]
qc1:
label: qc1
doc: Quality control for fastq file (fq1) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: pfastq_dump/forward
nthreads: nthreads
out: [qc]
qc2:
label: qc2
doc: Quality control for fastq file (fq2) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: pfastq_dump/reverse
nthreads: nthreads
out: [qc]
trimPE:
label: trimPE
doc: adaptor trimming
run: ../Tools/trimmomaticPE.cwl
in:
fq1: pfastq_dump/forward
fq2: pfastq_dump/reverse
out: [trimFq1P, trimFq2P]
qc1P:
label: qc1P
doc: Quality control for fastq file (fq1) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq1P
nthreads: nthreads
out: [qc]
qc2P:
label: qc2P
doc: Quality control for fastq file (fq2) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq2P
nthreads: nthreads
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]
sam2bam:
label: sam2bam
doc: Convert SAM to BAM
run: ../Tools/samtools-sam2bam.cwl
in:
sam: map/sam
out: [bam]
sort:
label: sort
doc: Sort BAM
run: ../Tools/samtools-sort.cwl
in:
bam: sam2bam/bam
out: [sorted-bam]
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
bam:
type: File
outputSource: sam2bam/bam
osort:
type: File
outputSource: sort/sorted-bam
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