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class: Workflow
cwlVersion: v1.2
id: sort-concat
label: sort-concat
inputs:
- id: msin
type: Directory[]
steps:
- id: sort_concatmap
in:
- id: msin
source: msin
out:
- id: filenames
- id: groupnames
- id: logfile
run: ../steps/sort_concatmap.cwl
label: sort_concatmap
- id: concatenate
in:
- id: msin
source:
- msin
- id: group_id
source: sort_concatmap/groupnames
- id: groups_specification
source: sort_concatmap/filenames
out:
- id: msout
- id: logfile
run: ./subworkflows/concatenation.cwl
scatter: group_id
label: concatenation
- id: concatenate_logfiles_concatenate
in:
- id: file_list
source:
- concatenate/logfile
- id: file_prefix
default: concatenate
out:
- id: output
run: ../steps/concatenate_files.cwl
label: concatenate_logfiles_concatenate
- id: save_logfiles
in:
- id: files
linkMerge: merge_flattened
source:
- sort_concatmap/logfile
- concatenate_logfiles_concatenate/output
- id: sub_directory_name
default: 'sort-concat'
out:
- id: dir
run: ../steps/collectfiles.cwl
label: save_logfiles
outputs:
- id: logdir
outputSource: save_logfiles/dir
type: Directory
- id: msout
outputSource: concatenate/msout
type: Directory[]
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement