feat: add testing for multiple execution modes

OpenOmics · Jul 17, 2024 · 0e00d8b · 0e00d8b
1 parent 5347491
commit 0e00d8b
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Showing 3 changed files with 41 additions and 3 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -10,21 +10,49 @@ on:
     branches_ignore: []
 
 jobs:
-  Dry_Run_and_Lint:
+  Dry_Run_and_Lint_DNA&RNA:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
     - uses: docker://snakemake/snakemake:latest
-    - name: Dry Run with test data
+    - name: Dry Run 
       run: |
         docker run -v $PWD:/opt2 snakemake/snakemake:latest \
         /opt2/metamorph run --input /opt2/.tests/test_cohort.txt \
         --output /opt2/output --mode local --dry-run
-    - name: View the pipeline config file
+    - name: View the pipeline config file [DNA & RNA modes]
       run: |
         echo "Generated config file for pipeline...." && cat $PWD/output/config.json
     - name: Lint Workflow
       continue-on-error: true
       run: |
         docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
         echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
+  Dry_Run_and_Lint_DNAonly1:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: docker://snakemake/snakemake:latest
+    - name: Dry Run [DNA only mode]
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:latest \
+        /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly.txt \
+        --output /opt2/output --mode local --dry-run
+    - name: View the pipeline config file [DNA only mode]
+      run: |
+        echo "Generated config file for pipeline...." && cat $PWD/output/config.json
+    - name: Lint Workflow
+      continue-on-error: true
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
+        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
+  Dry_Run_DNA2:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: docker://snakemake/snakemake:latest
+    - name: Dry Run [DNA only mode w RNA column]
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:latest \
+        /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly_RNAcolexists.txt \
+        --output /opt2/output --mode local --dry-run
diff --git a/.tests/test_cohort_DNAonly.txt b/.tests/test_cohort_DNAonly.txt
@@ -0,0 +1,5 @@
+DNA
+/opt2/.tests/WT_S1_R1.fastq.gz
+/opt2/.tests/WT_S1_R2.fastq.gz
+/opt2/.tests/WT_S2_R1.fastq.gz
+/opt2/.tests/WT_S2_R2.fastq.gz
diff --git a/.tests/test_cohort_DNAonly_RNAcolexists.txt b/.tests/test_cohort_DNAonly_RNAcolexists.txt
@@ -0,0 +1,5 @@
+DNA	RNA
+/opt2/.tests/WT_S1_R1.fastq.gz	
+/opt2/.tests/WT_S1_R2.fastq.gz	
+/opt2/.tests/WT_S2_R1.fastq.gz	
+/opt2/.tests/WT_S2_R2.fastq.gz