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cwlVersion: v1.1
class: CommandLineTool
$namespaces:
arv: "http://arvados.org/cwl#"
requirements:
DockerRequirement:
dockerFile: |
FROM debian:10
RUN apt-get update && apt-get -yq --no-install-recommends install samtools python3-rdflib
dockerImageId: rdflib-and-samtools
ResourceRequirement:
ramMin: 768
arv:RuntimeConstraints:
keep_cache: 2048
outputDirType: keep_output_dir
inputs:
script:
type: File
default:
class: File
location: from_sparql.py
metadata: File
fasta:
type: File
secondaryFiles: [.fai]
query: string
stdout: selected.fasta
outputs:
selected: stdout
arguments: [python3, $(inputs.script), $(inputs.metadata), $(inputs.fasta), $(inputs.query)]
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