Chore: updating CI to include dry-run with new options

OpenOmics · Apr 5, 2024 · 6f484c0 · 6f484c0
1 parent c6e757f
commit 6f484c0
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -25,6 +25,18 @@ jobs:
         /opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \
         /opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \
         --output /opt2/output --mode local --dry-run
+    - name: Dry Run with test data using all cli options 
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
+        /opt2/mpox-seek run --input \
+        /opt2/.tests/WT_S1_0.fastq.gz /opt2/.tests/WT_S1_1.fastq.gz \
+        /opt2/.tests/WT_S2_0.fastq.gz /opt2/.tests/WT_S2_1.fastq.gz \
+        /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
+        /opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \
+        /opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \
+        --output /opt2/output --mode local --batch-id 2024-04-03 \
+        --additional-strains resources/mpox_additional_strains.fa.gz \
+        --dry-run
     - name: View the pipeline config file
       run: |
         echo "Generated config file for pipeline...." && cat $PWD/output/config.json