From 1ba59836b06548d7c18dd1ca9d3fb574e2569b58 Mon Sep 17 00:00:00 2001 From: m-jahn Date: Thu, 18 Dec 2025 13:48:15 +0100 Subject: [PATCH] fix: update to apptainer workflow --- .github/workflows/deploy_apptainer.yml | 6 ------ .github/workflows/main.yml | 2 +- workflow/Snakefile | 2 +- 3 files changed, 2 insertions(+), 8 deletions(-) diff --git a/.github/workflows/deploy_apptainer.yml b/.github/workflows/deploy_apptainer.yml index e7b8081..1034cc3 100644 --- a/.github/workflows/deploy_apptainer.yml +++ b/.github/workflows/deploy_apptainer.yml @@ -20,12 +20,6 @@ jobs: with: fetch-depth: 0 - - name: add apptainer source - shell: bash - run: | - sudo add-apt-repository -y ppa:apptainer/ppa - sudo apt-get update - - name: create dockerfile uses: snakemake/snakemake-github-action@v2 with: diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index db11319..2d5653d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -53,4 +53,4 @@ jobs: with: directory: .test snakefile: workflow/Snakefile - args: "--report report.zip" + args: "--cores 2 --report report.zip" diff --git a/workflow/Snakefile b/workflow/Snakefile index fb02f75..38ec062 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -21,7 +21,7 @@ include: "rules/report.smk" # container definition (optional) # ----------------------------------------------------- -container: "oras://ghcr.io/mpusp/snakemake-simple-mapping:latest" +containerized: "oras://ghcr.io/mpusp/snakemake-simple-mapping:latest" # optional messages, log and error handling