Test with docker container

dfornika · dfornika · commit 0613a2d9bcd3 · 2025-05-29T15:14:14.000-07:00
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
@@ -4,7 +4,6 @@ set -eo pipefail
 
 nextflow run main.nf \
 	 -profile "${PROFILE}" \
-	 --cache ${HOME}/.conda/envs \
 	 --assembly_input .github/data/assemblies \
 	 --outdir .github/data/test_output \
 	 --collect_outputs \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -19,6 +19,9 @@ jobs:
           - nextflow_version: "24.10.6"
             java_version: "17"
             profile: "conda"
+	  - nextflow_version: "24.10.6"
+            java_version: "17"
+            profile: "docker"
     name: Nextflow v${{ matrix.nextflow_version }} / ${{ matrix.profile }}
     runs-on: ubuntu-latest
     steps:
diff --git a/nextflow.config b/nextflow.config
@@ -58,4 +58,8 @@ profiles {
 	    apptainer.cacheDir = params.cache
 	}
     }
+    docker {
+        docker.enabled = true
+	process.container = "ghcr.io/bccdc-phl/mlst-nf:faf21e8ae18de0c2"
+    }
 }

Original file line number	Diff line number	Diff line change
`@@ -58,4 +58,8 @@ profiles {`
`58`	`58`	`apptainer.cacheDir = params.cache`
`59`	`59`	`}`
`60`	`60`	`}`
	`61`	`+ docker {`
	`62`	`+ docker.enabled = true`
	`63`	`+ process.container = "ghcr.io/bccdc-phl/mlst-nf:faf21e8ae18de0c2"`
	`64`	`+ }`
`61`	`65`	`}`