feat: add methylation pipelines #786
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| name: Workflows Lint Check | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| import_syntax_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Check import syntax | |
| run: | | |
| EXITCODE=0 | |
| shopt -s extglob | |
| for file in $(find ./!(template) -name '*.wdl'); do | |
| >&2 echo "Checking file $file..." | |
| import_lines=$(awk '/import/' "$file" | grep -v '# lint-check: ignore') || true | |
| bad_lines=$(echo "$import_lines" | awk '/https:\/\/raw.githubusercontent.com\/stjudecloud\/workflows/') || true | |
| if [ -n "$bad_lines" ]; then | |
| >&2 echo "Imports from this repo must use relative paths!" | |
| >&2 echo "The following lines are bad:" | |
| >&2 echo "$bad_lines" | |
| >&2 echo "" | |
| EXITCODE=1 | |
| fi | |
| bad_lines=$(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 $EXITCODE | |
| docker_pull_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Ensure current SemVer'd docker images are being pulled | |
| run: | | |
| EXITCODE=0 | |
| files=$(find docker/ -name Dockerfile) | |
| for file in $files; do | |
| echo "$file" | awk -F '/' '{print tolower($2) ":" $3}' >> valid_dockerimages.txt | |
| done | |
| files=$(find . -name '*.wdl') | |
| for file in $files; do | |
| while IFS= read -r line; do | |
| tag=$(echo "$line" | awk -F ':' '{print substr($3, 1, length($3)-1)}') | |
| tool=$(echo "$line" | awk -F ':' '{print substr($2, 23, length($2)) ":" substr($3, 1, length($3)-1)}') | |
| case `grep -Fx "$tool" valid_dockerimages.txt >/dev/null; echo $?` in | |
| 0) | |
| # valid docker image | |
| ;; | |
| 1) | |
| >&2 echo "Must use a current Docker image" | |
| >&2 echo "Offending line: $line" | |
| >&2 echo "In file: $file" | |
| EXITCODE=1 | |
| ;; | |
| *) | |
| >&2 echo "Something went wrong while checking for current Docker images!" | |
| EXITCODE=2 | |
| ;; | |
| esac | |
| done < <(awk '/docker: .*stjudecloud/' < "$file") | |
| done | |
| exit $EXITCODE |