blob: 367b9bfa56be47e57ff401977327e1badfadcfd6 (
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|
cwlVersion: v1.1
class: CommandLineTool
inputs:
readsFA: File[]
subjects: string[]
exclude:
type: File?
inputBinding: {position: 2}
script:
type: File
default: {class: File, location: relabel-seqs.py}
inputBinding: {position: 1}
outputs:
relabeledSeqs:
type: File
outputBinding:
glob: relabeledSeqs.fasta
originalLabels:
type: File
outputBinding:
glob: originalLabels.ttl
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing: |
${
var i = 0;
var b = 1;
var out = [];
for (; i < inputs.readsFA.length; i++) {
var block = [];
var sub = [];
for (; i < (b*150) && i < inputs.readsFA.length; i++) {
block.push(inputs.readsFA[i]);
sub.push(inputs.subjects[i]);
}
out.push({
entryname: "block"+b,
entry: JSON.stringify(block)
});
out.push({
entryname: "subs"+b,
entry: JSON.stringify(sub)
});
b++;
}
return out;
}
hints:
DockerRequirement:
dockerPull: commonworkflowlanguage/cwltool_module
stdout:
baseCommand: [python]
|
