From e624988a38f9b0cfa9128940522773d0cb0fc3a1 Mon Sep 17 00:00:00 2001 From: Benjamin Date: Fri, 16 Jan 2026 13:51:40 -0800 Subject: [PATCH 1/2] Update all deeptools conda environment YAML files to version 3.5.6 Updating to version 3.5.6 bypasses a previous bug where deeptools version 3.5.5 is not compatible with NumPy version 2, but the bioconda recipe (meta.yaml; https://github.com/bioconda/bioconda-recipes/blob/591f3c411db2cb334511f0f13e60b4d4d9cadb2f/recipes/deeptools/meta.yaml) for deeptools version 3.5.5 only specifies a lower limit on NumPy versions (numpy >=1.9.0), which inadvertently allows conda to install NumPy version 2 and deeptools version 3.5.5 in the same environment, leading to incompatibilities and pipeline errors. --- modules/nf-core/deeptools/alignmentsieve/environment.yml | 3 +-- modules/nf-core/deeptools/bamcoverage/environment.yml | 3 +-- modules/nf-core/deeptools/bigwigcompare/environment.yml | 4 +++- modules/nf-core/deeptools/computematrix/environment.yml | 2 +- modules/nf-core/deeptools/multibamsummary/environment.yml | 2 +- modules/nf-core/deeptools/multibigwigsummary/environment.yml | 2 ++ modules/nf-core/deeptools/plotcorrelation/environment.yml | 2 +- modules/nf-core/deeptools/plotfingerprint/environment.yml | 2 +- modules/nf-core/deeptools/plotheatmap/environment.yml | 2 +- modules/nf-core/deeptools/plotpca/environment.yml | 2 +- modules/nf-core/deeptools/plotprofile/environment.yml | 2 +- 11 files changed, 14 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/deeptools/alignmentsieve/environment.yml b/modules/nf-core/deeptools/alignmentsieve/environment.yml index 40bec9452ad6..9d079059386d 100644 --- a/modules/nf-core/deeptools/alignmentsieve/environment.yml +++ b/modules/nf-core/deeptools/alignmentsieve/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 - - bioconda::samtools=1.20 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/bamcoverage/environment.yml b/modules/nf-core/deeptools/bamcoverage/environment.yml index 40bec9452ad6..9d079059386d 100644 --- a/modules/nf-core/deeptools/bamcoverage/environment.yml +++ b/modules/nf-core/deeptools/bamcoverage/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 - - bioconda::samtools=1.20 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/bigwigcompare/environment.yml b/modules/nf-core/deeptools/bigwigcompare/environment.yml index 7b72fdd99676..9d079059386d 100644 --- a/modules/nf-core/deeptools/bigwigcompare/environment.yml +++ b/modules/nf-core/deeptools/bigwigcompare/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.6" + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/computematrix/environment.yml b/modules/nf-core/deeptools/computematrix/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/computematrix/environment.yml +++ b/modules/nf-core/deeptools/computematrix/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/multibamsummary/environment.yml b/modules/nf-core/deeptools/multibamsummary/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/multibamsummary/environment.yml +++ b/modules/nf-core/deeptools/multibamsummary/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/multibigwigsummary/environment.yml b/modules/nf-core/deeptools/multibigwigsummary/environment.yml index d755dfc6bae7..9d079059386d 100644 --- a/modules/nf-core/deeptools/multibigwigsummary/environment.yml +++ b/modules/nf-core/deeptools/multibigwigsummary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeptools/plotcorrelation/environment.yml b/modules/nf-core/deeptools/plotcorrelation/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/plotcorrelation/environment.yml +++ b/modules/nf-core/deeptools/plotcorrelation/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/plotfingerprint/environment.yml b/modules/nf-core/deeptools/plotfingerprint/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/plotfingerprint/environment.yml +++ b/modules/nf-core/deeptools/plotfingerprint/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/plotheatmap/environment.yml b/modules/nf-core/deeptools/plotheatmap/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/plotheatmap/environment.yml +++ b/modules/nf-core/deeptools/plotheatmap/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/plotpca/environment.yml b/modules/nf-core/deeptools/plotpca/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/plotpca/environment.yml +++ b/modules/nf-core/deeptools/plotpca/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 diff --git a/modules/nf-core/deeptools/plotprofile/environment.yml b/modules/nf-core/deeptools/plotprofile/environment.yml index 0c80282ff2ef..9d079059386d 100644 --- a/modules/nf-core/deeptools/plotprofile/environment.yml +++ b/modules/nf-core/deeptools/plotprofile/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::deeptools=3.5.5 + - bioconda::deeptools=3.5.6 From 174ddc5a3b938fe2a09f145a8096eefa11c2ed2d Mon Sep 17 00:00:00 2001 From: Benjamin Date: Mon, 19 Jan 2026 13:11:21 -0800 Subject: [PATCH 2/2] Re-add samtools to deeptools/bamcoverage environment.yml --- modules/nf-core/deeptools/bamcoverage/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/deeptools/bamcoverage/environment.yml b/modules/nf-core/deeptools/bamcoverage/environment.yml index 9d079059386d..34c2d62a6c29 100644 --- a/modules/nf-core/deeptools/bamcoverage/environment.yml +++ b/modules/nf-core/deeptools/bamcoverage/environment.yml @@ -5,3 +5,4 @@ channels: - bioconda dependencies: - bioconda::deeptools=3.5.6 + - bioconda::samtools=1.23