/
hisat2-cufflinks_wf_pe.cwl
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hisat2-cufflinks_wf_pe.cwl
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cwlVersion: v1.0
class: Workflow
inputs:
## Common input
nthreads: int
## Inputs for download-sra
repo: string?
run_ids: string[]
## Inputs for hisat2_mapping
hisat2_idx_basedir: Directory
hisat2_idx_basename: string
## Inputs for cufflinks
annotation: File
outputs:
cufflinks_result:
type:
type: array
items: File
outputSource: cufflinks/cufflinks_result
steps:
download-sra:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/download-sra/download-sra.cwl
in:
repo: repo
run_ids: run_ids
out:
[sraFiles]
pfastq-dump:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/pfastq-dump/pfastq-dump.cwl
in:
sraFiles: download-sra/sraFiles
nthreads: nthreads
out:
[forward, reverse]
hisat2_mapping:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/hisat2/mapping/paired_end/hisat2_mapping_pe.cwl
in:
hisat2_idx_basedir: hisat2_idx_basedir
hisat2_idx_basename: hisat2_idx_basename
fq1: pfastq-dump/forward
fq2: pfastq-dump/reverse
nthreads: nthreads
out:
[hisat2_sam]
samtools_sam2bam:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/samtools/sam2bam/samtools_sam2bam.cwl
in:
input_sam: hisat2_mapping/hisat2_sam
out: [bamfile]
samtools_sort:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/samtools/sort/samtools_sort.cwl
in:
input_bam: samtools_sam2bam/bamfile
nthreads: nthreads
out: [sorted_bamfile]
cufflinks:
run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/cufflinks/cufflinks.cwl
in:
nthreads: nthreads
annotation: annotation
input_bam: samtools_sort/sorted_bamfile
out: [cufflinks_result]
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
s:license: https://spdx.org/licenses/Apache-2.0
s:codeRepository: https://github.com/pitagora-network/pitagora-cwl
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0003-3777-5945
s:email: mailto:inutano@gmail.com
s:name: Tazro Ohta
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf
- http://edamontology.org/EDAM_1.18.owl