FastQC: add dockerfile and environment.yml

.github/workflows/docker.yml

@@ -19,20 +19,26 @@ jobs:
       # Find the tool wrappers that changed
       # Annoyingly, matrix can't take dynamic variables
       - name: Find changed tools
-        run: TOOLS=$( git diff --name-only $GITHUB_SHA | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF )
+        run: |
-
+          TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF )
-
+          echo "Tools that appear to have been updated:"
+          echo $TOOLS
+          # Save so that GitHub Actions can see this variable in the next step
+          echo "::set-env name=TOOLS::$TOOLS"
 
       - name: Build images
         run: |
+          echo "Running the docker build"
+          echo $TOOLS
           for d in tools/*; do
+            echo "In directory $d"
             for TOOL in $TOOLS; do
-              $TOOL
+              echo "Tool is $TOOL"
               if echo $d/ | grep -q "$TOOL"; then
                 cd "$GITHUB_WORKSPACE/$d"
                 TOOLNAME=$(basename `pwd`)
                 IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
-                echo $IMGNAME
+                echo "Image name is: $IMGNAME"
                 docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com
                 docker build -t $IMGNAME  .
                 docker push $IMGNAME

tools/fastqc/Dockerfile

@@ -0,0 +1,7 @@
+FROM nfcore/base:1.7
+LABEL authors="phil.ewels@scilifelab.se" \
+      description="Docker image for nf-core modules fastqc"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-modules-fastqc/bin:$PATH

tools/fastqc/environment.yml

@@ -0,0 +1,9 @@
+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-modules-fastqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - fastqc=0.11.8