/
wf_bacterial_noncoding.cwl
executable file
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/
wf_bacterial_noncoding.cwl
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#!/usr/bin/env cwl-runner
label: "Non-Coding Bacterial Genes"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
inputs:
asn_cache: Directory
seqids: File
16s_blastdb_dir: Directory
23s_blastdb_dir: Directory
model_path: File
rfam_amendments: File
rfam_stockholm: File
taxon_db: File
outputs:
# asncache:
# type: Directory
# outputSource: bacterial_noncoding_16S/asncache
annotations_5s:
type: File
outputSource: bacterial_noncoding_5S/annots
annotations_16s:
type: File
outputSource: bacterial_noncoding_16S/annotations
annotations_23s:
type: File
outputSource: bacterial_noncoding_23S/annotations
steps:
bacterial_noncoding_5S:
run: wf_gcmsearch.cwl
in:
asn_cache: asn_cache
seqids: seqids
model_path: model_path
rfam_amendments: rfam_amendments
rfam_stockholm: rfam_stockholm
taxon_db: taxon_db
out: [ annots ]
bacterial_noncoding_16S:
run: wf_blastn.cwl
in:
asn_cache: asn_cache
seqids: seqids
blastdb_dir: 16s_blastdb_dir
blastdb:
default: blastdb
product_name:
default: "16S ribosomal RNA"
outname:
default: annotations_16s.asn
out: [annotations]
bacterial_noncoding_23S:
run: wf_blastn.cwl
in:
asn_cache: asn_cache
seqids: seqids
blastdb_dir: 23s_blastdb_dir
blastdb:
default: Ribosom23S
product_name:
default: "23S ribosomal RNA"
outname:
default: annotations_23s.asn
out: [annotations]