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collate_unique_SSU_headers.cwl
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collate_unique_SSU_headers.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
ScatterFeatureRequirement: {}
inputs:
hits: File[]
outputs:
unique_hits:
type: File
outputSource: sort_uniq_names/sorted_uniq_names
steps:
extract_coord_lines:
run: extract_coord_lines.cwl
in: { summary: hits }
scatter: summary
out: [ coord_lines ]
extract_names:
run:
id: extract_names # TODO, remove when toil upgrade to a newer cwltool
class: CommandLineTool
inputs:
coordinate_lines:
type: File
inputBinding: { position: 1 }
doc: |
The required columns are as follows:
(1) target name: The name of the target sequence or profile.
baseCommand: [ awk, '{print $1}' ]
stdout: names # helps with cwltool's --cache
outputs: { names: { type: stdout } }
in: { coordinate_lines: extract_coord_lines/coord_lines }
scatter: coordinate_lines
out: [ names ]
sort_uniq_names:
run:
id: sort_uniq_names # TODO, remove when toil upgrades to a newer cwltool
class: CommandLineTool
inputs:
names:
type: File[]
inputBinding: { position: 1 }
baseCommand: [ sort, --unique ]
stdout: sorted_uniq_names # helps with cwltool's --cache
outputs: { sorted_uniq_names: stdout }
in: { names: extract_names/names }
out: [ sorted_uniq_names ]
$namespaces:
s: http://schema.org/
$schemas:
- https://schema.org/docs/schema_org_rdfa.html
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"