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rRNA_selection.cwl
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rRNA_selection.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
indexed_sequences:
type: File
secondaryFiles: .ssi
format: edam:format_1929 # FASTA
model:
type: File
format: edam:format_1370 # HMMER
label: rRNA protein model to search with
outputs:
matching_sequences:
type: File
format: edam:format_1929 # FASTA
outputSource: fetch_aligned_sequences/sequences
hmmer_search_results:
type: File
outputSource: hmmsearch/per_domain_summary
steps:
hmmsearch:
run: hmmsearch.cwl
in:
hmm_profiles: model
sequence_query: indexed_sequences
e_threshold: { default: "1.0E-5" }
out: [ per_domain_summary ]
extract_coord_lines:
run: extract_coord_lines.cwl
in: { summary: hmmsearch/per_domain_summary }
out: [ coord_lines ]
extract_coordinates:
run:
id: extract_coordinates # TODO, remove when toil upgrade to a newer cwltool
class: CommandLineTool
inputs:
coordinate_lines:
type: File
inputBinding: { position: 1 }
streamable: true
doc: |
The required columns are as follows:
(1) target name: The name of the target sequence or profile.
(18) from (ali coord): The start of the MEA alignment of this
domain with respect to the sequence, numbered 1..L for a
sequence of L residues.
(19) to (ali coord): The end of the MEA alignment of this domain
with respect to the sequence, numbered 1..L for a sequence of
L residues.
baseCommand: [ awk, '{print $1"/"$18"-"$19" "$18" "$19" "$1}' ]
stdout: formatted_names_and_coords # helps with cwltool's --cache
outputs: { formatted_names_and_coords: { type: stdout } }
in: { coordinate_lines: extract_coord_lines/coord_lines }
out: [ formatted_names_and_coords ]
fetch_aligned_sequences:
run: esl-sfetch-manyseqs.cwl
in:
indexed_sequences: indexed_sequences
names: extract_coordinates/formatted_names_and_coords
names_contain_subseq_coords: { default: true }
out: [ sequences ]
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$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"