From 98a1f66ccf02298a68cb62d53fa11904294acfa5 Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Tue, 7 Apr 2026 20:32:34 +0200 Subject: [PATCH 1/2] Fix CI: update mamba-org/setup-micromamba to v2 --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 14e8071..39558df 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@v4 - name: conda/mamba - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v2 with: environment-file: environment.yml create-args: >- From 02f17878d32ebcd8cf118e64252531dc0ec8efae Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Thu, 21 May 2026 14:09:42 +0200 Subject: [PATCH 2/2] update containers --- sequana_pipelines/mapper/config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sequana_pipelines/mapper/config.yaml b/sequana_pipelines/mapper/config.yaml index 8314851..c26571f 100644 --- a/sequana_pipelines/mapper/config.yaml +++ b/sequana_pipelines/mapper/config.yaml @@ -23,14 +23,14 @@ apptainers: bamtools: https://zenodo.org/record/10211475/files/bamtools_2.5.2.img bowtie2: https://zenodo.org/record/8037162/files/sequana_minimal_23.6.13.img bwa: https://zenodo.org/record/8037162/files/sequana_minimal_23.6.13.img - deeptools: https://zenodo.org/record/7341710/files/sequana_tools_0.14.5.img + deeptools: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img graphviz: https://zenodo.org/record/7928262/files/graphviz_7.0.5.img - minimap2: https://zenodo.org/record/7341710/files/sequana_tools_0.14.5.img + minimap2: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img multiqc: https://zenodo.org/record/10205070/files/multiqc_1.16.0.img samtools: https://zenodo.org/record/7437898/files/samtools_1.16.1.img sequana_coverage: https://zenodo.org/record/13946414/files/sequana_coverage_0.18.0.img seqkit: https://zenodo.org/record/7821924/files/seqkit_2.4.0.img - subread: https://zenodo.org/record/7341710/files/sequana_tools_0.14.5.img + subread: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img mosdepth: https://zenodo.org/record/12805460/files/mosdepth_0.3.8.img