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executable file 36 lines (29 sloc) 761 Bytes
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
inputs:
proteins_to_align: File
nucleotides: File
outputs:
alignment1: { type: File, outputSource: clustal/alignment }
guide_tree: { type: File, outputSource: clustal/guide_tree }
alignment2: { type: File, outputSource: pal2nal/alignment }
results: { type: File, outputSource: codeml/results }
steps:
clustal:
run: clustalo.cwl
in:
multi_sequence: proteins_to_align
out: [alignment, guide_tree]
pal2nal:
run: pal2nal.cwl
in:
protein_alignment: clustal/alignment
nucleotides: nucleotides
out: [alignment]
codeml:
run: codeml.cwl
in:
seq: pal2nal/alignment
tree: clustal/guide_tree
out: [results]
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