/
wf_gcmsearch.cwl
executable file
·53 lines (46 loc) · 1.21 KB
/
wf_gcmsearch.cwl
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#!/usr/bin/env cwl-runner
label: "Run genomic CMsearch (Rfam rRNA)"
cwlVersion: v1.0
class: Workflow
#requirements:
inputs:
go:
type: boolean[]
asn_cache: Directory
seqids: File
model_path: File
rfam_amendments: File
rfam_stockholm: File
taxon_db: File
outputs:
annots:
type: File
outputSource: Post_process_CMsearch_Rfam_annotations/annots
steps:
Run_genomic_CMsearch_Rfam_rRNA_submit:
run: gpx_qsubmit.cwl
in:
asn_cache: asn_cache
seqids: seqids
out: [jobs]
Run_genomic_CMsearch_Rfam_rRNA_wnode:
run: cmsearch_wnode.cwl
in:
asn_cache: asn_cache
input_jobs: Run_genomic_CMsearch_Rfam_rRNA_submit/jobs
model_path: model_path
rfam_amendments: rfam_amendments
rfam_stockholm: rfam_stockholm
taxon_db: taxon_db
out: [outdir]
Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump:
run: gpx_qdump.cwl
in:
input_path: Run_genomic_CMsearch_Rfam_rRNA_wnode/outdir
out: [annots]
Post_process_CMsearch_Rfam_annotations:
run: annot_merge.cwl
in:
asn_cache: asn_cache
input: Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump/annots
out: [annots]