From 503e267806e8c40fffe3439e023afff25ea0067e Mon Sep 17 00:00:00 2001 From: Katherine Heal Date: Fri, 15 Nov 2024 12:32:31 -0800 Subject: [PATCH] Combine CI/CD into one gh workflow --- .github/workflows/wdl_checker.yml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/.github/workflows/wdl_checker.yml b/.github/workflows/wdl_checker.yml index 404ebcd..2618fb5 100644 --- a/.github/workflows/wdl_checker.yml +++ b/.github/workflows/wdl_checker.yml @@ -17,15 +17,24 @@ jobs: with: python-version: '3.8' # specify the Python version you need + - name: Install Docker + run: | + curl -fsSL https://get.docker.com -o get-docker.sh + sh get-docker.sh + sudo usermod -aG docker $USER + + - name: Build Docker Image + run: | + docker build -t local-metams:latest . + - name: Install MiniWDL run: | python -m pip install --upgrade pip pip install miniwdl -# TODO KRH: Add these back in once the WDL and docker images are ready -# - name: Test LCMS Lipid MiniWDL -# run: | -# miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json + - name: Test Lipid MiniWDL + run: | + miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files - name: Test GCMS MiniWDL run: |