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Go back to hardcoding WDL files in CI
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I couldn't get the dynamic detection to work, so go back to the
simple method.
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amstilp committed May 29, 2024
1 parent db1c449 commit c265671
Showing 1 changed file with 9 additions and 26 deletions.
35 changes: 9 additions & 26 deletions .github/workflows/womtool.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,36 +20,19 @@ concurrency:

jobs:

detect-wdl-files:
runs-on: ubuntu-latest
name: "Detect WDL files"
outputs:
matrix: ${{ steps.detect-files.outputs.matrix }}

steps:

- name: Checkout Code Repository
uses: actions/checkout@v4

- name: Detect WDL files
id: detect-files
run: |
# Find the WDL files
wdl_files=`find . -name "*.wdl" -type f -print0 | xargs -0`
# Add double quotes and replace spaces with commas.
wdl_files=\"${wdl_files// /\",\"}\"
echo "matrix={\"wdl-file\":[$wdl_files]" >> $GITHUB_OUTPUT
- name: Show WDL files
run: echo "${{ steps.detect-files.outputs.matrix }}"

run-womtool:
needs: detect-wdl-files
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix: ${{ fromJSON(needs.detect-wdl-files.outputs.matrix) }}
matrix:
wdl-file: [
./gsr_data_report.wdl,
./check_vcf_samples.wdl,
./pheno_qc/pheno_qc.wdl,
./validate_genotype_model.wdl,
./validate_gsr_model.wdl,
./validate_phenotype_model.wdl,
]

name: "Run womtool: ${{ matrix.wdl-file }}"

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