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Pull request overview
This PR consolidates the GENERATE_GENOME subworkflow structure by combining three separate subworkflows into one, updates version output formatting for Perl scripts and Python modules to use a new tuple-based system, and removes version output from the repeat density subworkflow. The changes also include adding an enum constraint for the map_order parameter in the input schema.
Changes:
- Consolidated GENERATE_GENOME* subworkflows (3 → 1) by removing separate sorted/unsorted genome workflows
- Updated version outputs across multiple modules to use tuple-based format with standardized version extraction
- Added enum validation for
map_orderparameter in schema_input.json
Reviewed changes
Copilot reviewed 27 out of 27 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| workflows/treeval.nf | Removed version mixing from REPEAT_DENSITY subworkflow |
| tests/default.nf.test.snap | Updated test snapshots to reflect new version output format |
| subworkflows/local/selfcomp/main.nf | Removed version mixing calls for SPLITFASTA and MUMMER2BED processes |
| subworkflows/local/repeat_density/main.nf | Removed version channel initialization and output, added whitespace formatting |
| subworkflows/local/read_coverage/main.nf | Removed version mixing for GRAPH_OVERALL_COVERAGE and FIND_HALF_COVERAGE, added whitespace |
| subworkflows/local/insilico_digest/main.nf | Removed version mixing for MAKECMAP modules |
| subworkflows/local/generate_unsorted_genome/main.nf | Deleted entire file as part of consolidation |
| subworkflows/local/generate_sorted_genome/main.nf | Deleted entire file as part of consolidation |
| subworkflows/local/generate_genome/main.nf | Consolidated logic from deleted subworkflows, simplified channel handling |
| modules/local/selfcomp/splitfasta/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/selfcomp/mummer2bed/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/selfcomp/mapids/main.nf | Updated tag syntax and simplified Python version extraction |
| modules/local/selfcomp/alignmentblocks/main.nf | Updated tag syntax and simplified Python version extraction |
| modules/local/pretext/graph/main.nf | Updated tag syntax from double quotes |
| modules/local/makecmap/renamecmapids/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/makecmap/fa2cmapmulticolor/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/makecmap/cmap2bed/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/graph/overall_coverage/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/get/paired_contact_bed/main.nf | Updated tag syntax from double quotes |
| modules/local/find/half_coverage/main.nf | Updated tag syntax and converted to tuple-based version outputs |
| modules/local/extract/repeat/main.nf | Updated tag syntax, converted to tuple-based version outputs, updated version to 1.0.0 |
| modules/local/extract/ancestral/main.nf | Updated tag syntax from double quotes |
| modules/local/cram/filter_minimap2_filter5end_fixmate_sort/main.nf | Updated tag syntax from double quotes |
| modules/local/cram/filter_align_bwamem2_fixmate_sort/main.nf | Updated tag syntax from double quotes |
| modules/local/bamtobed/sort/main.nf | Updated tag syntax from double quotes |
| modules/local/assign/ancestral/main.nf | Updated tag syntax from double quotes |
| assets/schema_input.json | Added enum constraint for map_order parameter and reformatted existing enums |
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Copilot caught a copy paste issue Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Update the GENERATE_GENOME* subworkflow (3 subworkflows down into 1)
Update the version outputs of the perl scripts + 1 python module.
No more version output from the repeat density subworkflow.
Manually updated the snapshot
Added an enum for the
map_order