/
genomics-workspace.cwl
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/
genomics-workspace.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
- class: SubworkflowFeatureRequirement
inputs:
scientific_name: string[]
tree: string[]
managePy_Path: string
blastdb_Path: string[]
hmmerdb_Path: string[]
in_fasta: File
in_fasta_protein: File[]
in_fasta_transcript: File
in_fasta_cds: File
steps:
#step 1
genomics-workspace-genome:
run: genomics-workspace-genome.cwl
in:
in_fasta: in_fasta
scientific_name: scientific_name
managePy_Path: managePy_Path
blastdb_Path: blastdb_Path
tree: tree
out:
[out_dummy]
#step 2
genomics-workspace-protein:
run: genomics-workspace-protein.cwl
in:
in_fasta_protein: in_fasta_protein
scientific_name: scientific_name
tree: tree
managePy_Path: managePy_Path
blastdb_Path: blastdb_Path
hmmerdb_Path: hmmerdb_Path
in_dummy: genomics-workspace-genome/out_dummy
out:
[]
#step 3
genomics-workspace-transcript:
run: genomics-workspace-transcript.cwl
in:
in_fasta_transcript: in_fasta_transcript
scientific_name: scientific_name
tree: tree
managePy_Path: managePy_Path
blastdb_Path: blastdb_Path
in_dummy: genomics-workspace-genome/out_dummy
out:
[]
#step 4
genomics-workspace-cds:
run: genomics-workspace-cds.cwl
in:
in_fasta_cds: in_fasta_cds
scientific_name: scientific_name
tree: tree
managePy_Path: managePy_Path
blastdb_Path: blastdb_Path
in_dummy: genomics-workspace-genome/out_dummy
out:
[]
outputs: []