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gem.cwl
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/
gem.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
label: "GEM peak calling"
doc: "This workflow execute peak calling using GEM"
inputs:
threads: int
infile: File
chromsize: File
mapsize: int
format: string
genome_dir: Directory
k_min: int
k_max: int
smooth: int
k_seqs: int
outputs:
gem_out:
outputSource: gem/output
type: Directory
steps:
gzip_cat:
run: ../../tools/basic/gzip.cwl
in:
d: { default: True}
file: infile
out: [output]
gem:
run: ../../tools/gem/gem.cwl
in:
t: threads
s: mapsize
g: chromsize
d: { default: "Read_Distribution_ChIP-exo.txt"}
expt: gzip_cat/output
f: format
genome: genome_dir
k_min: k_min
k_max: k_max
k_seqs: k_seqs
outNP: { default: True}
smooth: smooth
out:
valueFrom: ${ return inputs.expt.nameroot.replace('.tagAlign','_gem');}
out: [output]
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-4108-5982
s:email: mailto:r78v10a07@gmail.com
s:name: Roberto Vera Alvarez
s:license: https://spdx.org/licenses/OPL-1.0
$namespaces:
s: http://schema.org/
$schemas:
- https://schema.org/version/latest/schema.rdf