diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 945ae006..f630898a 100644 --- a/.github/workflows/docker.yml +++ b/.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 $IMGNAME diff --git a/tools/fastqc/Dockerfile b/tools/fastqc/Dockerfile new file mode 100644 index 00000000..6428b03e --- /dev/null +++ b/tools/fastqc/Dockerfile @@ -0,0 +1,7 @@ +FROM nfcore/base:1.7 +LABEL authors="phil.ewels@scilifelab.se" \ + description="Docker image for nf-core modules fastqc" + +COPY environment.yml / +RUN conda env create -f /environment.yml && conda clean -a +ENV PATH /opt/conda/envs/nf-core-modules-fastqc/bin:$PATH diff --git a/tools/fastqc/environment.yml b/tools/fastqc/environment.yml new file mode 100644 index 00000000..0f438e8b --- /dev/null +++ b/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