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cwlVersion: v1.1
class: CommandLineTool
inputs:
readsFA: File[]
outputs:
readsMergeDedup:
type: File
outputBinding:
glob: readsMergeDedup.fasta
dups:
type: File
outputBinding:
glob: dups.txt
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/seqkit:0.7.1--0"
ResourceRequirement:
coresMin: 8
coresMax: 32
ramMin: $(7 * 1024)
outdirMin: |
${
var sum = 0;
for (var i = 0; i < inputs.readsFA.length; i++) {
sum += inputs.readsFA[i].size;
}
return (sum/(1024*1024*1024)+1) + 20;
}
baseCommand: seqkit
arguments: [rmdup,
--by-seq,
--ignore-case,
--dup-num-file, dups.txt,
-o, readsMergeDedup.fasta,
$(inputs.readsFA)]
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