diff --git a/action.yml b/action.yml index 01db76b..0ae6c36 100644 --- a/action.yml +++ b/action.yml @@ -56,9 +56,17 @@ runs: sudo apt-get update sudo apt-get install -y apptainer - - name: Prepare environment.yaml + - name: Prepare .snakemake.environment.yaml shell: bash -el {0} - run: sed 's/{{ snakemake_version }}/${{ inputs.snakemake-version }}/g' environment.yaml.template > environment.yaml + run: |8 + cat < .snakemake.environment.yaml + channels: + - conda-forge + - bioconda + - nodefaults + dependencies: + - snakemake ==${{ inputs.snakemake-version }} + EOF - name: Setup conda uses: conda-incubator/setup-miniconda@v3 @@ -66,7 +74,7 @@ runs: channels: conda-forge,bioconda channel-priority: strict miniforge-version: latest - environment-file: environment.yaml + environment-file: .snakemake.environment.yaml activate-environment: snakemake - name: Display snakemake version