From 03632972f55983385f903cfa955604b62c4ec883 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Wed, 19 Jul 2023 13:25:23 +0100
Subject: [PATCH] add singularity

---
 .github/workflows/ci.yml                 |  6 +-
 .github/workflows/preload-containers.yml | 78 ++++++++++++++++++++++++
 .github/workflows/preload-docker.yml     | 32 ----------
 3 files changed, 81 insertions(+), 35 deletions(-)
 create mode 100644 .github/workflows/preload-containers.yml
 delete mode 100644 .github/workflows/preload-docker.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 345ba949..5883ca93 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,11 +13,11 @@ on:
     types: [published]
 
 jobs:
-  preload_docker:
-    uses: ./.github/workflows/preload-docker.yml
+  preload_containers:
+    uses: ./.github/workflows/preload-containers.yml
     
   test:
-    needs: preload_docker
+    needs: preload_containers
     name: Run standard workflow test
     runs-on: ubuntu-latest
     env:
diff --git a/.github/workflows/preload-containers.yml b/.github/workflows/preload-containers.yml
new file mode 100644
index 00000000..8e32eda2
--- /dev/null
+++ b/.github/workflows/preload-containers.yml
@@ -0,0 +1,78 @@
+name: Preload docker containers
+
+on:
+  workflow_call:
+    inputs:
+      singularity_version:
+        required: true
+        type: string
+    outputs:
+      docker-cache-key:
+        value: docker-${{ github.sha }}
+      singularity-cache-key:
+        value: singularity-${{ github.sha }}
+
+env:
+  NXF_SINGULARITY_CACHEDIR: "${{ github.workspace }}/singularity"
+  SINGULARITY_VERSION: "3.8.3"
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Pull and save docker
+        run: |
+          git grep 'ext.docker*' ${{ github.workspace }}/conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > ${{ runner.temp }}/images.txt
+          cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker pull --platform linux/amd64 "$1"' - {}
+          mkdir -p ${{ runner.temp }}/docker/
+          cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker save "$1" > ${{ runner.temp }}/docker/$(basename "$1").tar' - {}
+
+      - name: Save docker
+        id: cache-docker
+        uses: actions/cache@v3
+        with:
+          path: ${{ runner.temp }}/docker
+          key: docker-${{ github.sha }}
+
+  singularity:
+    runs-on: ubuntu-latest
+    steps:          
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Cache singularity setup
+        id: cache-singularity-setup
+        uses: actions/cache@v3
+        with:
+          path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
+          key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
+
+      - name: Set up Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        if: ${{ steps.cache-singularity-setup.outputs.cache-hit != 'true' }}
+        with:
+          singularity-version: ${{ env.SINGULARITY_VERSION }}
+
+      - name: Add singularity to path
+        if: steps.cache-singularity-setup.outputs.cache-hit == 'true'
+        run: |
+          echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH
+
+      - name: Pull and save singularity
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          git grep 'ext.singularity*' conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > ${{ runner.temp }}/singularity_images.txt
+          cat ${{ runner.temp }}/singularity_images.txt | sed 's/oras:\/\///;s/https:\/\///;s/\//-/g;s/$/.img/;s/:/-/' > ${{ runner.temp }}/singularity_image_paths.txt
+          paste -d '\n' ${{ runner.temp }}/singularity_image_paths.txt ${{ runner.temp }}/singularity_images.txt | xargs -L 2 sh -c 'singularity pull --disable-cache --dir $NXF_SINGULARITY_CACHEDIR $0 $1'
+
+      - name: Cache singularity images
+        id: cache-singularity-pull
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
+          key: singularity-${{ github.sha }}
+          
+          
diff --git a/.github/workflows/preload-docker.yml b/.github/workflows/preload-docker.yml
deleted file mode 100644
index 0f6ce44d..00000000
--- a/.github/workflows/preload-docker.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-name: Preload singularity and docker containers
-
-on:
-  workflow_call:
-    outputs:
-      docker-cache-key:
-        description: "Docker cache key"
-        value: ${{ github.sha }}
-        
-jobs:
-  docker:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Pull and save docker
-        run: |
-          git grep 'ext.docker*' ${{ github.workspace }}/conf/modules.config | cut -f 2 -d '=' | xargs -L 2 echo | tr -d ' ' > ${{ runner.temp }}/images.txt
-          cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker pull --platform linux/amd64 "$1"' - {}
-          mkdir -p ${{ runner.temp }}/docker/
-          cat ${{ runner.temp }}/images.txt | xargs -I {} sh -c 'docker save "$1" > ${{ runner.temp }}/docker/$(basename "$1").tar' - {}
-
-      - name: Save docker
-        id: cache-docker
-        uses: actions/cache@v3
-        with:
-          path: ${{ runner.temp }}/docker
-          key: ${{ github.sha }}
-          
-          
-