Add docker profile for tests (#33)

* Test with docker container

* whitespace

* filter out WARNING generated using apptainer/docker profile

Author: dfornika

.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 \

.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:

modules/quast.nf

@@ -14,7 +14,7 @@ process quast {
     printf -- "- process_name: quast\\n"                  >> ${sample_id}_quast_provenance.yml
     printf -- "  tools:\\n"                               >> ${sample_id}_quast_provenance.yml
     printf -- "    - tool_name: quast\\n"                 >> ${sample_id}_quast_provenance.yml
-    printf -- "      tool_version: \$(quast --version | cut -d ' ' -f 2 | tr -d 'v')\\n" >> ${sample_id}_quast_provenance.yml
+    printf -- "      tool_version: \$(quast --version | grep --invert-match '^WARNING' | cut -d ' ' -f 2 | tr -d 'v')\\n" >> ${sample_id}_quast_provenance.yml
     printf -- "      parameters:\\n"                      >> ${sample_id}_quast_provenance.yml
     printf -- "        - parameter: --space-efficient\\n" >> ${sample_id}_quast_provenance.yml
     printf -- "          value: null\\n"                  >> ${sample_id}_quast_provenance.yml

nextflow.config

@@ -58,4 +58,8 @@ profiles {
 	    apptainer.cacheDir = params.cache
 	}
     }
+    docker {
+        docker.enabled = true
+	process.container = "ghcr.io/bccdc-phl/mlst-nf:faf21e8ae18de0c2"
+    }
 }