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cmsearch-multimodel-wf.cwl
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cmsearch-multimodel-wf.cwl
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cwlVersion: v1.0
class: Workflow
$namespaces:
edam: 'http://edamontology.org/'
s: 'http://schema.org/'
label: Identifies non-coding RNAs using Rfams covariance models
requirements:
- class: ScatterFeatureRequirement
inputs:
clan_info:
type: File
cores:
type: int
covariance_models:
type: File[]
query_sequences:
type: File
catOutputFileName:
type: string
default: cat_cmsearch_matches.tbl
outputs:
cmsearch_matches:
outputSource: cmsearch/matches
type: File[]
concatenate_matches:
outputSource: run_concatenate_matches/result
type: File
deoverlapped_matches:
outputSource: remove_overlaps/deoverlapped_matches
type: File
steps:
cmsearch:
label: Search sequence(s) against a covariance model database
run: ../tools/Infernal/cmsearch/infernal-cmsearch-v1.1.2.cwl
in:
covariance_model_database: covariance_models
cpu: cores
omit_alignment_section:
default: true
only_hmm:
default: true
query_sequences: query_sequences
search_space_size:
default: 1000
scatter: covariance_model_database
out: [ matches, programOutput ]
run_concatenate_matches:
run: ../utils/concatenate.cwl
in:
files: cmsearch/matches
outputFileName: catOutputFileName
out: [ result ]
remove_overlaps:
label: Remove lower scoring overlaps from cmsearch --tblout files.
run: ../tools/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl
in:
clan_information: clan_info
cmsearch_matches: run_concatenate_matches/result
out: [ deoverlapped_matches ]
$schemas:
- 'http://edamontology.org/EDAM_1.16.owl'
- 'https://schema.org/docs/schema_org_rdfa.html'
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute, 2018"
s:author: "Arnaud Meng, Maxim Scheremetjew"