Prepare 4.0.0.-alpha release

.github/workflows/docker.yml

@@ -9,33 +9,35 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       -
         name: Sanitize Repo Name for Tagging
         run: echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]' | (read; echo REPO_LOWER=$REPLY) >> $GITHUB_ENV
       - 
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
       - 
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
       - 
         name: Login to Docker Hub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - 
         name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ secrets.GH_USERNAME }}
           password: ${{ secrets.GH_TOKEN }}
       - name: Build and Push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           push: true
           tags: |
             ghcr.io/${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+            ghcr.io/${{ env.REPO_LOWER }}:latest
             ${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+            ${{ env.REPO_LOWER }}:latest

.github/workflows/docker_branches.yml

@@ -2,15 +2,15 @@ name: Publish Docker image
 on:
   push:
     branches-ignore:
-    - 'master'
+    - 'main'
 
 jobs:
   push_to_registry:
     name: Push Docker image to Docker Hub
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       -
         name: Sanitize Repo Name for Tagging
         run: echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]' | (read; echo REPO_LOWER=$REPLY) >> $GITHUB_ENV
@@ -25,18 +25,18 @@ jobs:
             type=ref,event=pr
       - 
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
       - 
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
       - 
         name: Login to Docker Hub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Push to Docker Hub
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           push: true
           tags: ${{ steps.meta.outputs.tags }}

.github/workflows/lint-check.yml

@@ -3,49 +3,40 @@ name: lint-check
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 jobs:
   import_syntax_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Check import syntax
       run: |
         EXITCODE=0
         for file in $(find . -name '*.wdl'); do
           >&2 echo "Checking file $file..."
           import_lines=$(awk '/import/' "$file")
-          bad_lines=$(echo "$import_lines" | awk '!/https:\/\/raw.githubusercontent.com\/stjude\/xenocp\/master/ && !/https:\/\/raw.githubusercontent.com\/stjudecloud\/workflows\/master/' | grep -v '# lint-check: ignore') || true
+
+          bad_lines=$(echo "$import_lines" | awk '/https:\/\/raw.githubusercontent.com\/stjude\/XenoCP/') || true
           if [ -n "$bad_lines" ]; then
-            >&2 echo "Must import files from the master branch on Github."
+            >&2 echo "Imports from this repo must use relative paths!"
             >&2 echo "The following lines are bad:"
             >&2 echo "$bad_lines"
             >&2 echo ""
             EXITCODE=1
           fi
-        done
-        exit $EXITCODE
-  docker_pull_check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Ensure SemVer'd docker images are being pulled
-      run: |
-        EXITCODE=0
-        files=$(find . -name '*.wdl')
-        for file in $files; do
-          while IFS= read -r line; do
-            tag=$(echo "$line" | awk -F ':' '{print substr($3, 1, length($3)-1)}')
-            if ! [[ $tag =~ ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(-(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(\.(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*)?(\+[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*)?$ ]]; then
-              >&2 echo "All Docker containers must be using an official SemVer tagged image"
-              >&2 echo "Offending line: $line"
-              >&2 echo "In file: $file"
-              EXITCODE=1
-            fi
-          done < <(awk '/docker: .*stjudecloud/ || /docker: .*stjude/' < "$file")
+
+          bad_lines=$(echo "$import_lines" | awk '/http/ && (/main/ || /master/)') || true
+          if [ -n "$bad_lines" ]; then
+            >&2 echo "Imports from external repos must use a tagged release!"
+            >&2 echo "The following lines are bad:"
+            >&2 echo "$bad_lines"
+            >&2 echo ""
+            EXITCODE=1
+          fi
+
         done
         exit $EXITCODE

.github/workflows/miniwdl-check.yml

@@ -6,11 +6,11 @@ jobs:
   miniwdl_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.6'
+        python-version: '3.10'
     - name: Install miniwdl
       run: |
         python -m pip install --upgrade pip
@@ -20,10 +20,7 @@ jobs:
         EXITCODE=0
         echo "Checking WDL files using \`miniwdl check\`."
         files=$(find . -name '*.wdl')
-        for file in $files; do
-          sed -i 's,https://raw.githubusercontent.com/stjude/xenocp/'"$(echo ${GITHUB_REF#refs/heads/})"','"$(pwd)"',g' "$file"
-          sed -i 's,https://raw.githubusercontent.com/stjude/xenocp/master,'"$(pwd)"',g' "$file"
-        done
+
         for file in $files; do
           echo "  [***] $file [***]"
           miniwdl check "$file"

.github/workflows/release-check.yml

@@ -0,0 +1,31 @@
+name: release-check
+
+on:
+  push:
+    branches:
+      - release
+  pull_request:
+    branches:
+      - release
+
+jobs:
+  docker_pull_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Ensure SemVer'd docker images are being pulled
+      run: |
+        EXITCODE=0
+        files=$(find . -name '*.wdl')
+        for file in $files; do
+          while IFS= read -r line; do
+            tag=$(echo "$line" | awk -F ':' '{print substr($3, 1, length($3)-1)}')
+            if ! [[ $tag =~ ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(-(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(\.(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*)?(\+[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*)?$ ]]; then
+              >&2 echo "All Docker containers must be using an official SemVer tagged image"
+              >&2 echo "Offending line: $line"
+              >&2 echo "In file: $file"
+              EXITCODE=1
+            fi
+          done < <(awk '/docker: .*stjudecloud/ || /docker: .*stjude/' < "$file")
+        done
+        exit $EXITCODE

Dockerfile

@@ -1,4 +1,6 @@
-FROM ubuntu:18.04 as builder
+FROM ubuntu:20.04 as builder
+
+ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update \
     && apt-get --yes install \
@@ -73,7 +75,7 @@ RUN cd /tmp/xenocp \
     && gradle installDist \
     && cp -r build/install/xenocp /opt
 
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 RUN apt-get update \
     && apt-get --yes install --no-install-recommends \
@@ -82,6 +84,7 @@ RUN apt-get update \
         openjdk-11-jre-headless \
         python3 \
         python3-distutils \
+        python-is-python3 \
         file \
     && rm -rf /var/lib/apt/lists/*
 
@@ -98,4 +101,4 @@ COPY --from=builder /opt/xenocp/bin/* /usr/local/bin/
 
 COPY cwl /opt/xenocp/cwl
 
-ENTRYPOINT ["cwl-runner", "--parallel", "--outdir", "results", "/opt/xenocp/cwl/xenocp.cwl"]
+ENTRYPOINT ["cwl-runner", "--parallel", "--outdir", "results", "--no-container", "/opt/xenocp/cwl/xenocp.cwl"]

RELEASE.md

@@ -0,0 +1,5 @@
+# Release
+
+  * [ ] Update version in `dx_app/dxapp.json`.
+  * [ ] Update `wdl/tools/xenocp.wdl` with version.
+  * [ ] Update `wdl/workflows/xenocp.wdl` with version.

bin/picard

@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+java -jar /opt/picard/lib/picard*.jar "$@"

cwl/bwa_mem_onlymapped.cwl

@@ -12,6 +12,11 @@ hints:
       tweak_sam:
         specs: ["java.sh org.stjude.compbio.sam.TweakSam"]
 
+requirements:
+  ResourceRequirement:
+    ramMin: 15000
+    coresMin: 1
+
 inputs:
   ref_db_prefix: 
     type: string

cwl/cat.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+doc: |
+  Merge a set of files into file using the cat utility.
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+baseCommand: cat
+
+inputs:
+  output_file:
+    type: string
+    doc: |
+      Name of final file.
+
+  input_files:
+    type: File[]
+    inputBinding:
+      position: 4
+    doc: |
+      Array of files to merge. 
+
+stdout: $(inputs.output_file)
+
+outputs:
+  combined_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_file)