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genomics-workspace-genome.cwl
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genomics-workspace-genome.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
inputs:
scientific_name: string[]
in_fasta: File
managePy_Path: string
blastdb_Path: string[]
tree: string[]
steps:
#step 0
addfile_2_db:
run: addfile_2_db.cwl
in:
in_fasta: in_fasta
blastdb_Path: blastdb_Path
out:
[out_dummy]
#step 1
addorganism:
run: addorganism.cwl
in:
scientific_name: scientific_name
managePy_Path: managePy_Path
in_dummy: addfile_2_db/out_dummy
out:
[out_dummy]
#step 2
addblast:
run: addblast-genome.cwl
in:
scientific_name: scientific_name
managePy_Path: managePy_Path
in_fasta: in_fasta
in_dummy: addorganism/out_dummy
tree: tree
out:
[out_dummy]
#step 3
makeblastdb:
run: makeblastdb.cwl
in:
in_fasta: in_fasta
managePy_Path: managePy_Path
in_dummy: addblast/out_dummy
out:
[out_dummy]
#step 4
populatesequence:
run: populatesequence.cwl
in:
in_fasta: in_fasta
managePy_Path: managePy_Path
in_dummy: makeblastdb/out_dummy
out:
[out_dummy]
#step 5
showblast:
run: showblast.cwl
in:
in_fasta: in_fasta
managePy_Path: managePy_Path
in_dummy: populatesequence/out_dummy
out:
[out_dummy]
outputs:
out_dummy:
type: File
outputSource: addorganism/out_dummy