From f36ed3f516cd282f0d08c8c17ba6171be3580832 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 4 Apr 2024 12:22:52 +0100
Subject: [PATCH] Add pre-fetch for the containers in ascc with nf-download

---
 .github/workflows/ci.yml | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bdce0f5..f0675ba 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,6 +10,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -27,6 +29,12 @@ jobs:
           - "22.10.1"
           - "latest-everything"
     steps:
+      - name: Get branch names
+        # Pulls the names of current branches in repo
+        # steps.branch-names.outputs.current_branch is used later and returns the name of the branch the PR is made FROM not to
+        id: branch-names
+        uses: tj-actions/branch-names@v8
+
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
@@ -35,6 +43,27 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - 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/ascc --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-ascc --container-cache-utilisation amend --container-system docker
+
       - name: Download test data
         # Download A fungal test data set that is full enough to show some real output.
         run: |
@@ -89,7 +118,7 @@ jobs:
           mkdir vecscreen
           curl -L https://ftp.ncbi.nlm.nih.gov/blast/db/v4/16SMicrobial_v4.tar.gz | tar -C vecscreen -xzf -
 
-      - name: Run pipeline with test data
+      - name: Singularity - Run FULL pipeline with test data
         # 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