From ba6b661e6866b427a0531b5a193491bd7ee0ed7a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 10 Oct 2024 16:22:05 +0200
Subject: [PATCH] fix GHA

---
 .../.github/workflows/ci.yml                  | 61 ++++++++++++++++---
 1 file changed, 51 insertions(+), 10 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index cddac0d45..7fc18a245 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -11,26 +11,44 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: {% raw %}${{ github.workspace }}{% endraw %}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: {% raw %}${{ github.workspace }}{% endraw %}/.singularity
 
 concurrency:
-  group: "{% raw %}${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}{% endraw %}"
+  group: "{% raw %}${{ github.workflow }}{% endraw %}-{% raw %}${{ github.event.pull_request.number || github.ref }}{% endraw %}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data ({% raw %}${{ matrix.NXF_VER }}{% endraw %} | {% raw %}${{ matrix.test }}{% endraw %} | {% raw %}${{ matrix.profile }}{% endraw %})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "{% raw %}${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}{% endraw %}"
+    if: "{% raw %}${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bamtofastq') }}{% endraw %}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        engine:
+        profile:
           - "conda"
           - "docker"
           - "singularity"
+        test:
+          - "test"
+          - "test_cram"
+          - "test_chr"
+          - "test_no_bai"
+          - "test_no_crai"
+          - "test_no_stats"
+          - "test_no_qc"
+          - "test_collate_fast"
+        isMaster:
+          - {% raw %}${{ github.base_ref == 'master' }}{% endraw %}
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -40,13 +58,36 @@ jobs:
         with:
           version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}"
 
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          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
+          channels: conda-forge,bioconda
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline with test data {% raw %}${{ matrix.NXF_VER }}{% endraw %} | {% raw %}${{ matrix.engine }}{% endraw %}"
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: " Run pipeline with test data {% raw %}${{ matrix.NXF_VER }}{% endraw %} | {% raw %}${{ matrix.test }}{% endraw %} | {% raw %}${{ matrix.profile }}{% endraw %}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,{% raw %}${{ matrix.engine }}{% endraw %} --outdir ./results
-          if: "!{% raw %}${{ github.base_ref == 'master' }}{% endraw %} || {% raw %}${{ matrix.engine == 'docker' }}{% endraw %}"
+          nextflow run ${GITHUB_WORKSPACE} -profile {% raw %}${{ matrix.test }}{% endraw %},{% raw %}${{ matrix.profile }}{% endraw %} --outdir ./results