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subample-pseudoreplicates.cwl
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subample-pseudoreplicates.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
label: "Subsample BAM file creating a tagAlign and pseudoreplicates"
doc: "This workflow creates a subsample from a BAM file creating a tagAlign and pseudoreplicates"
inputs:
bam_file: File
nreads: int
outputs:
tagalign_out:
outputSource: create_tagalign/output
type: File
subsample_out:
outputSource: gzip/output
type: File
pseudoreplicate_gzip_out:
outputSource: pseudoreplicate_gzip/output
type: File[]
steps:
create_tagalign:
run: create-tagAlign.cwl
in:
bam_file: bam_file
out: [output]
gzip_cat:
run: ../../tools/basic/gzip.cwl
in:
c: { default: True}
d: { default: True}
file: create_tagalign/output
outFileName:
valueFrom: ${ return inputs.file.nameroot;}
out: [output]
filter_chrM:
run: ../../tools/basic/grep.cwl
in:
v: { default: True }
outFileName:
valueFrom: ${ return inputs.file.nameroot;}
pattern: { default: 'chrM' }
file: gzip_cat/output
out: [output]
shuf:
run: ../../tools/basic/shuf.cwl
in:
n: nreads
outFileName:
valueFrom: ${ return inputs.file.nameroot + ".filt.nodup.sample.tagAlign";}
random-source: gzip_cat/output
file: filter_chrM/output
out: [output]
gzip:
run: ../../tools/basic/gzip.cwl
in:
c: { default: True }
n: { default: True }
file: shuf/output
outFileName:
valueFrom: ${ return inputs.file.basename + ".gz";}
out: [output]
pseudoreplicate_count_lines:
run: ../../tools/basic/wc.cwl
in:
l: { default: True }
file: gzip_cat/output
outFileName:
valueFrom: ${ return inputs.file.nameroot;}
out: [output]
pseudoreplicate_split_file:
run: ../../tools/basic/split_half.cwl
in:
d: { default: True}
valuefile: pseudoreplicate_count_lines/output
file: gzip_cat/output
outFileName:
valueFrom: ${ return inputs.file.nameroot + '.';}
out: [output]
pseudoreplicate_gzip:
run: ../../tools/basic/gzip.cwl
scatter: [file]
in:
c: { default: True }
file: pseudoreplicate_split_file/output
outFileName:
valueFrom: ${ return inputs.file.basename + '.tagAlign.gz';}
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
$namespaces:
s: http://schema.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf