forked from EBI-Metagenomics/ebi-metagenomics-cwl
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cmsearch-multimodel.cwl
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/
cmsearch-multimodel.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
ScatterFeatureRequirement: {}
inputs:
query_sequences: File
covariance_models: File[]
clan_info: File
outputs:
matches:
type: File
outputSource: remove_overlaps/deoverlapped_matches
steps:
cmsearch:
run: ../tools/infernal-cmsearch.cwl
in:
query_sequences: query_sequences
covariance_model_database: covariance_models
only_hmm: { default: true }
omit_alignment_section: { default: true }
search_space_size: { default: 1000 }
out: [ matches ]
scatter: covariance_model_database
concatenate_matches:
run: ../tools/concatenate.cwl
in:
files: cmsearch/matches
out: [ result ]
remove_overlaps:
run: ../tools/cmsearch-deoverlap.cwl
in:
cmsearch_matches: concatenate_matches/result
clan_information: clan_info
out: [ deoverlapped_matches ]