From e852649647c91b0d486c7b85e3c80603fc878335 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Wed, 12 Jun 2024 14:13:09 +0000 Subject: [PATCH] Testing execution on slurm --- .github/workflows/main_test.yaml | 2 +- workflow/envs/ashleys_base.yaml | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main_test.yaml b/.github/workflows/main_test.yaml index 8c3c9fb..223fa0c 100644 --- a/.github/workflows/main_test.yaml +++ b/.github/workflows/main_test.yaml @@ -130,7 +130,7 @@ jobs: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http snakemake-executor-plugin-slurm - name: Run workflow run: | - snakemake -j 4 --executor slurm --software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile + snakemake -j 1 -c 4 --executor slurm --software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile # Testing_ashleys_with_custom_python_singularity: # runs-on: ubuntu-latest diff --git a/workflow/envs/ashleys_base.yaml b/workflow/envs/ashleys_base.yaml index 5cc8561..82218c4 100644 --- a/workflow/envs/ashleys_base.yaml +++ b/workflow/envs/ashleys_base.yaml @@ -17,3 +17,5 @@ dependencies: - multiqc # Fix sklearn update - scikit-learn=1.2.2 + # Fix ashleys GH issue + - python=3.10