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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
$graph:
- id: rnaseq
class: CommandLineTool
inputs:
sequence: string
outputs:
seqout: stdout
arguments: [echo, $(inputs.sequence)]
stdout: rnaseq
- id: cat
class: CommandLineTool
inputs:
sequences: File[]
catfilename: string
outputs:
catout: stdout
arguments: [cat, $(inputs.sequences)]
stdout: $(inputs.catfilename)
- id: tr
class: CommandLineTool
inputs:
trinput: File
from: string
to: string
filename: string
outputs:
trout: stdout
arguments: [tr, $(inputs.from), $(inputs.to)]
stdin: $(inputs.trinput.path)
stdout: $(inputs.filename)
- id: main
class: Workflow
inputs:
rna: string[]
outputs:
outfile:
type: File
outputSource: translate_sequences/trout
requirements:
- class: ScatterFeatureRequirement
steps:
get_sequences:
run: "#rnaseq"
scatter: sequence
in:
sequence: rna
out: [seqout]
combine_sequences:
run: "#cat"
in:
sequences: get_sequences/seqout
catfilename: { default: "database.dna" }
out: [catout]
translate_sequences:
run: "#tr"
in:
trinput: combine_sequences/catout
from: { default: "U" }
to: { default: "T" }
filename: { default: "database.dna" }
out: [trout]