/
mashmap_swf.cwl
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/
mashmap_swf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: MashMap
doc: MashMap sub-worklow
requirements:
StepInputExpressionRequirement: {}
ScatterFeatureRequirement: {}
InlineJavascriptRequirement: {}
inputs:
input_fastas:
type:
type: array
items: ["null", "File"]
format: edam:format_1929
doc: FASTA files
reference:
type: File?
steps:
mashmap:
run: mashmap.cwl
scatter: query
label: run mashmap
when: $(inputs.query !== null && inputs.query.nameroot && !inputs.query.nameroot.includes('empty_'))
in:
query: input_fastas
reference: reference
no_split:
valueFrom: $(true)
minimum_segment_length:
valueFrom: $(2000)
output_file:
valueFrom: |
${
if (inputs.query && inputs.query.nameroot) {
return inputs.query.nameroot + "_mashmap.out";
} else {
return "empty_mashmap.out";
}
}
out:
- mashmap_table
outputs:
output_table:
type: File[]
outputSource:
- mashmap/mashmap_table
pickValue: all_non_null
$namespaces:
s: http://schema.org/
edam: http://edamontology.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder:
- class: s:Organization
s:name: "EMBL - European Bioinformatics Institute"
s:url: "https://www.ebi.ac.uk"