From 56d5754522be5880efa3d96c488562c1fcdd987e Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 11:40:54 +0200 Subject: [PATCH 1/6] Update bcftools.yaml to remove gsl dependency comment * Removed gsl dependency comment in bcftools.yaml as bcftool pkg now includes correct libraries --- src/mmaseq/workflow/envs/bcftools.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/mmaseq/workflow/envs/bcftools.yaml b/src/mmaseq/workflow/envs/bcftools.yaml index a95fcdb4..6edfacbb 100644 --- a/src/mmaseq/workflow/envs/bcftools.yaml +++ b/src/mmaseq/workflow/envs/bcftools.yaml @@ -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 From 2cd19f1a531f9404fd6d331db5475f6f0d8885dc Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 11:43:05 +0200 Subject: [PATCH 2/6] Update serotypefinder.yaml --- src/mmaseq/workflow/envs/serotypefinder.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/mmaseq/workflow/envs/serotypefinder.yaml b/src/mmaseq/workflow/envs/serotypefinder.yaml index 02810ae5..da8c1941 100644 --- a/src/mmaseq/workflow/envs/serotypefinder.yaml +++ b/src/mmaseq/workflow/envs/serotypefinder.yaml @@ -1,4 +1,3 @@ name: serotypefinder dependencies: - bioconda::serotypefinder - - conda-forge::python=3.9 From 96125f511fa10502ade30687326c7c66978b79b3 Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 11:43:17 +0200 Subject: [PATCH 3/6] Remove duplicate dependencies in resfinder.yaml --- src/mmaseq/workflow/envs/resfinder.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/mmaseq/workflow/envs/resfinder.yaml b/src/mmaseq/workflow/envs/resfinder.yaml index a00169cf..8026bc67 100644 --- a/src/mmaseq/workflow/envs/resfinder.yaml +++ b/src/mmaseq/workflow/envs/resfinder.yaml @@ -1,4 +1,3 @@ name: resfinder dependencies: - bioconda::resfinder - - bioconda::kma From b25791cfbe2490891744e716eef318b6405a474d Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 11:43:30 +0200 Subject: [PATCH 4/6] Remove kma dependency from plasmidfinder.yaml --- src/mmaseq/workflow/envs/plasmidfinder.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/mmaseq/workflow/envs/plasmidfinder.yaml b/src/mmaseq/workflow/envs/plasmidfinder.yaml index 42a73285..a19b8afc 100644 --- a/src/mmaseq/workflow/envs/plasmidfinder.yaml +++ b/src/mmaseq/workflow/envs/plasmidfinder.yaml @@ -1,4 +1,3 @@ name: plasmidfinder dependencies: - bioconda::plasmidfinder - - bioconda::kma From b77f0503a93ec0d4b78537a1409293fe115935ad Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 11:43:49 +0200 Subject: [PATCH 5/6] Remove duplicate dependency entries in shovill.yaml --- src/mmaseq/workflow/envs/shovill.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/mmaseq/workflow/envs/shovill.yaml b/src/mmaseq/workflow/envs/shovill.yaml index 389f3b82..4bf05308 100644 --- a/src/mmaseq/workflow/envs/shovill.yaml +++ b/src/mmaseq/workflow/envs/shovill.yaml @@ -1,5 +1,3 @@ name: shovill dependencies: - - bioconda::spades - bioconda::shovill - From ade30323192839942e5f1ed4e29a0828f1bcae76 Mon Sep 17 00:00:00 2001 From: Kasper Thystrup Karstensen Date: Tue, 18 Aug 2026 15:55:23 +0200 Subject: [PATCH 6/6] Reinstated python depenency due to deprecetation dependency --- src/mmaseq/workflow/envs/serotypefinder.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/mmaseq/workflow/envs/serotypefinder.yaml b/src/mmaseq/workflow/envs/serotypefinder.yaml index da8c1941..02810ae5 100644 --- a/src/mmaseq/workflow/envs/serotypefinder.yaml +++ b/src/mmaseq/workflow/envs/serotypefinder.yaml @@ -1,3 +1,4 @@ name: serotypefinder dependencies: - bioconda::serotypefinder + - conda-forge::python=3.9