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| author | pjotrp | 2026-04-04 11:25:46 +0200 |
|---|---|---|
| committer | pjotrp | 2026-04-04 11:25:46 +0200 |
| commit | 4d968831509bb740d49c3bcbcdd42aeeb730a1ad (patch) | |
| tree | 9d47cab47a0c2c323dac209bc36ee348ab97a550 | |
| parent | 27dd15f8f0ada7670019f683d0cd76dd61bdda0f (diff) | |
| download | guix-bioinformatics-4d968831509bb740d49c3bcbcdd42aeeb730a1ad.tar.gz | |
Update tests so they pass for cosigt
| -rw-r--r-- | gn/packages/pangenome.scm | 6 |
1 files changed, 5 insertions, 1 deletions
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index c82b988..6c8e5d6 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -676,11 +676,15 @@ The path-guided stochastic gradient descent based 1D sort implemented in ;; --invert-filtering -> removed (substitute* "pggb" (("--approx-map\\b") "--approx-mapping") + ;; wfmash 0.24 defaults to -w 1000; pass -w = segment_length + ;; so short sequences aren't skipped + (("-l \\$block_length") + "-w $segment_length -l $block_length") (("-H \\$mash_kmer_thres") "") (("--hg-filter-ani-diff \\$hg_filter_ani_diff") "--hg-filter=$hg_filter_ani_diff,0.0,99.9") (("exclude_cmd=\"-Y \"\\$exclude_delim") - "exclude_cmd=\"-Y\"$exclude_delim") + "exclude_cmd=\"\"") (("--invert-filtering") "")))) (add-after 'install 'wrap-scripts (lambda* (#:key inputs outputs #:allow-other-keys) |