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move_and_validate_interleaved_fq.cwl
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move_and_validate_interleaved_fq.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
id: "move-and-validate-a-interleaved-fastq"
label: "A CGP workflow to move and validate an interleave fastq"
cwlVersion: v1.0
requirements:
MultipleInputFeatureRequirement: {}
StepInputExpressionRequirement: {}
inputs:
fastq_in:
type: File
doc: "A gzipped interleaved fastq file."
outputs:
interleaved_fastq_out:
type: File
format: edam:format_1930
outputSource: rename/outfile
report:
type: File
format: edam:format_3464
outputSource: validate/report_json
steps:
rename:
in:
srcfile:
source: fastq_in
newname:
source: fastq_in
valueFrom: $(self.basename)
out: [outfile]
run: rename.cwl
validate:
in:
fastqs_in:
source: [rename/outfile]
linkMerge: merge_flattened
out: [report_json]
run: cgp-seqval-qc_pairs.cwl
doc: |
A workflow to copy the input interleaved fastq file to a new place and validate the file format and base quality score range. See the [workflow-seq-import](https://github.com/cancerit/workflow-seq-import) website for more information.
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
- http://edamontology.org/EDAM_1.18.owl
$namespaces:
s: http://schema.org/
edam: http://edamontology.org/
s:codeRepository: https://github.com/cancerit/workflow-seq-import
s:license: https://spdx.org/licenses/AGPL-3.0
s:author:
- class: s:Person
s:email: mailto:yyaobo@gmail.com
s:name: Yaobo Xu
dct:creator:
foaf:name: Yaobo Xu
foaf:mbox: "yyaobo@gmail.com"