From abb72b9dda548501f172aa43eb5a743305a57894 Mon Sep 17 00:00:00 2001 From: yumisims Date: Fri, 24 May 2024 13:23:26 +0100 Subject: [PATCH] test --- .github/workflows/ci.yml | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 211262c..66a660c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,6 +47,27 @@ jobs: run: | nextflow secrets set NCBI_API_KEY ${{ secrets.NCBI_API_KEY }} + - name: Set up Singularity + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Install Python + uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Install nf-core + run: | + pip install nf-core + + - name: NF-Core Download - download singularity containers + # Forcibly download repo on active branch and download SINGULARITY containers into the CACHE dir if not found + # Must occur after singularity install or will crash trying to dl containers + # Zip up this fresh download and run the checked out version + run: | + nf-core download sanger-tol/genomeassembly --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-genomeassembly --container-cache-utilisation amend --container-system singularity + - name: Download test data run: | curl https://tolit.cog.sanger.ac.uk/test-data/resources/genomeassembly/genomeassembly_test_data.tar.gz | tar xzf - @@ -54,11 +75,6 @@ jobs: - name: Setup apptainer uses: eWaterCycle/setup-apptainer@main - - name: Set up Singularity - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Run pipeline with test data run: | nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity --outdir ./results