Wdl workflow (#23)

* Initial implementation of XenoCP workflow in WDL

* Implementing multiple mappers

* Initial implementation of XenoCP workflow in WDL

* Implementing multiple mappers

* Add explicit queryname sort step

* Update GitHub links

* Update wdl/tools/xenocp.wdl

Co-authored-by: Andrew Frantz <andrew.frantz@stjude.org>

* Implement @a-frantz suggestions

* Implement @a-frantz suggestions

* Add lint and miniwdl checks for WDL

* fix: typo

* remove unused CPU argument

* Swap Docker version to 3.1.0 in anticipation of new release

* Connect unused inputs and remove remaining unused options

Co-authored-by: Andrew Frantz <andrew.frantz@stjude.org>

Author: adthrasher

.github/workflows/lint-check.yml

@@ -0,0 +1,51 @@
+name: lint-check
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  import_syntax_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - 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 "$import_lines" | awk '!/https:\/\/raw.githubusercontent.com\/stjude\/xenocp\/master/ && !/https:\/\/raw.githubusercontent.com\/stjudecloud\/workflows\/master/' | grep -v '# lint-check: ignore') || true
+          if [ -n "$bad_lines" ]; then
+            >&2 echo "Must import files from the master branch on Github."
+            >&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")
+        done
+        exit $EXITCODE

.github/workflows/miniwdl-check.yml

@@ -0,0 +1,32 @@
+name: miniwdl-check
+
+on: [push]
+
+jobs:
+  miniwdl_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.6'
+    - name: Install miniwdl
+      run: |
+        python -m pip install --upgrade pip
+        pip install miniwdl
+    - name: Run miniwdl
+      run: |
+        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"
+          EXITCODE=$(($? || EXITCODE))
+        done
+        exit $EXITCODE