From c8ceddfe77e0ed96c45d33a2ec54f8c932957bf8 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 6 Mar 2020 14:03:13 +0000
Subject: [PATCH] Tidying, add samtools and trim_galore

---
 .github/workflows/docker.yml      | 25 ++++++++++++++++---------
 tools/fastqc/Dockerfile           |  1 +
 tools/samtools/Dockerfile         |  8 ++++++++
 tools/samtools/environment.yml    |  9 +++++++++
 tools/trim_galore/Dockerfile      |  8 ++++++++
 tools/trim_galore/environment.yml |  9 +++++++++
 6 files changed, 51 insertions(+), 9 deletions(-)
 create mode 100644 tools/samtools/Dockerfile
 create mode 100644 tools/samtools/environment.yml
 create mode 100644 tools/trim_galore/Dockerfile
 create mode 100644 tools/trim_galore/environment.yml

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index f630898a..c4a39fe1 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -20,26 +20,33 @@ jobs:
       # Annoyingly, matrix can't take dynamic variables
       - name: Find changed tools
         run: |
-          TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF )
-          echo "Tools that appear to have been updated:"
-          echo $TOOLS
+          TOOLS=$( git diff --name-only HEAD~ | egrep -o 'tools\/[^\/]+\/' | sort | uniq | awk NF | tr '\r\n' ' ' )
           # Save so that GitHub Actions can see this variable in the next step
           echo "::set-env name=TOOLS::$TOOLS"
+          echo "Tools that appear to have been updated:"
+          echo $TOOLS
+
 
       - name: Build images
         run: |
-          echo "Running the docker build"
-          echo $TOOLS
+          echo "Tools that appear to have been updated:"
+          echo -e $TOOLS
+          echo '-----'
+          for TOOL in $TOOLS; do
+            echo $TOOL
+          done;
+          echo '-----'
           for d in tools/*; do
-            echo "In directory $d"
             for TOOL in $TOOLS; do
-              echo "Tool is $TOOL"
+              echo "$d -- $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
+                # IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:$GITHUB_SHA
+                # TODO: How do we have a proper version tag here?
+                IMGNAME=docker.pkg.github.com/${GITHUB_REPOSITORY,,}/${TOOLNAME,,}:latest
                 echo "Image name is: $IMGNAME"
-                docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com
+                echo "${{ secrets.GITHUB_TOKEN }}" | docker login -u ${{ github.actor }} --password-stdin docker.pkg.github.com
                 docker build -t $IMGNAME  .
                 docker push $IMGNAME
               fi;
diff --git a/tools/fastqc/Dockerfile b/tools/fastqc/Dockerfile
index 6428b03e..a6f4f8ce 100644
--- a/tools/fastqc/Dockerfile
+++ b/tools/fastqc/Dockerfile
@@ -2,6 +2,7 @@ FROM nfcore/base:1.7
 LABEL authors="phil.ewels@scilifelab.se" \
       description="Docker image for nf-core modules fastqc"
 
+# foobar
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH /opt/conda/envs/nf-core-modules-fastqc/bin:$PATH
diff --git a/tools/samtools/Dockerfile b/tools/samtools/Dockerfile
new file mode 100644
index 00000000..3d5cf586
--- /dev/null
+++ b/tools/samtools/Dockerfile
@@ -0,0 +1,8 @@
+FROM nfcore/base:1.7
+LABEL authors="phil.ewels@scilifelab.se" \
+      description="Docker image for nf-core modules samtools"
+
+# foobar
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-modules-samtools/bin:$PATH
diff --git a/tools/samtools/environment.yml b/tools/samtools/environment.yml
new file mode 100644
index 00000000..1a909c80
--- /dev/null
+++ b/tools/samtools/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-samtools
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - samtools=1.9
diff --git a/tools/trim_galore/Dockerfile b/tools/trim_galore/Dockerfile
new file mode 100644
index 00000000..56f75baa
--- /dev/null
+++ b/tools/trim_galore/Dockerfile
@@ -0,0 +1,8 @@
+FROM nfcore/base:1.7
+LABEL authors="phil.ewels@scilifelab.se" \
+      description="Docker image for nf-core modules trimgalore"
+
+# foobar
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-modules-trimgalore/bin:$PATH
diff --git a/tools/trim_galore/environment.yml b/tools/trim_galore/environment.yml
new file mode 100644
index 00000000..f2a1f047
--- /dev/null
+++ b/tools/trim_galore/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-trimgalore
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - trim-galore=0.6.4