From 403ac2c26dc3a21e52564f0bcba1658f93677271 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= Date: Mon, 3 Mar 2025 14:10:52 +0000 Subject: [PATCH 1/4] updated ci to exlude conda --- .github/workflows/ci.yml | 41 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 21 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b643cf8..116d95b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,14 +35,7 @@ jobs: - "singularity" test_name: - "test" - isMaster: - - ${{ github.base_ref == 'master' }} - # Exclude conda and singularity on dev - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" + steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 @@ -64,24 +57,30 @@ jobs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda + # - name: Set up Miniconda + # if: matrix.profile == 'conda' + # uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + # with: + # miniconda-version: "latest" + # auto-update-conda: true + # conda-solver: libmamba + # channels: conda-forge,bioconda - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH + # - name: Set up Conda + # if: matrix.profile == 'conda' + # run: | + # echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + # echo $(realpath python) >> $GITHUB_PATH - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" + if: matrix.profile != 'conda' run: | nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results + + - name: "Skip conda test" + if: matrix.profile == 'conda' + run: | + echo "Skipping conda test" From 73b50a2bb79faf1b693e8fdabf384c76d1d277cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= Date: Mon, 3 Mar 2025 14:13:37 +0000 Subject: [PATCH 2/4] removed commented conda reference --- .github/workflows/ci.yml | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 116d95b..5a61171 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -57,21 +57,6 @@ jobs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - # - name: Set up Miniconda - # if: matrix.profile == 'conda' - # uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - # with: - # miniconda-version: "latest" - # auto-update-conda: true - # conda-solver: libmamba - # channels: conda-forge,bioconda - - # - name: Set up Conda - # if: matrix.profile == 'conda' - # run: | - # echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - # echo $(realpath python) >> $GITHUB_PATH - - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 From 419dfbb7ec02f7b76920a8d345ca4f578d1017e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= Date: Mon, 3 Mar 2025 14:19:21 +0000 Subject: [PATCH 3/4] skipping singularity on dev --- .github/workflows/ci.yml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5a61171..c5e5f8e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,7 +35,13 @@ jobs: - "singularity" test_name: - "test" - + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda overall and singularity on dev + exclude: + - profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 @@ -64,8 +70,3 @@ jobs: if: matrix.profile != 'conda' run: | nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results - - - name: "Skip conda test" - if: matrix.profile == 'conda' - run: | - echo "Skipping conda test" From 6e8a6b6a6471c18cce888306d5e658972f65a0e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?= Date: Mon, 3 Mar 2025 14:42:52 +0000 Subject: [PATCH 4/4] returned singularity testing to dev --- .github/workflows/ci.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c5e5f8e..d962c99 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -37,11 +37,9 @@ jobs: - "test" isMaster: - ${{ github.base_ref == 'master' }} - # Exclude conda overall and singularity on dev exclude: - profile: "conda" - - isMaster: false - profile: "singularity" + steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 @@ -67,6 +65,5 @@ jobs: uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" - if: matrix.profile != 'conda' run: | nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results