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Update bcftools.yaml to remove gsl dependency comment #222

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Update bcftools.yaml to remove gsl dependency comment #222

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56d5754
Update bcftools.yaml to remove gsl dependency comment
KasperThystrup Aug 18, 2026
2cd19f1
Update serotypefinder.yaml
KasperThystrup Aug 18, 2026
96125f5
Remove duplicate dependencies in resfinder.yaml
KasperThystrup Aug 18, 2026
b25791c
Remove kma dependency from plasmidfinder.yaml
KasperThystrup Aug 18, 2026
b77f050
Remove duplicate dependency entries in shovill.yaml
KasperThystrup Aug 18, 2026
ade3032
Reinstated python depenency due to deprecetation dependency
KasperThystrup Aug 18, 2026
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4 changes: 0 additions & 4 deletions src/mmaseq/workflow/envs/bcftools.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,3 @@
name: bcftools
dependencies:
- bioconda::bcftools
# BioConda bcftools incorrectly lists gsl >2.7 as a dependency,
# despite being compiled against 2.5. By adding this as a separate
# dependency, this will cause the correct .so file to be present.
- conda-forge::gsl=2.5
1 change: 0 additions & 1 deletion src/mmaseq/workflow/envs/plasmidfinder.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
name: plasmidfinder
dependencies:
- bioconda::plasmidfinder
- bioconda::kma
1 change: 0 additions & 1 deletion src/mmaseq/workflow/envs/resfinder.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
name: resfinder
dependencies:
- bioconda::resfinder
- bioconda::kma
2 changes: 0 additions & 2 deletions src/mmaseq/workflow/envs/shovill.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@
name: shovill
dependencies:
- bioconda::spades
- bioconda::shovill

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