Fix publishing prokka outputs (#51)

* Fix publishDir pattern for prokka outputs * Run prokka in tests * Fix artifacts name
BCCDC-PHL · May 16, 2024 · d014d32 · d014d32
1 parent 4353a05
commit d014d32
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
@@ -10,5 +10,6 @@ nextflow run main.nf \
 	 --cache ${HOME}/.conda/envs \
 	 --fastq_input .github/data/fastq \
 	 --outdir .github/data/test_output \
+	 --prokka \
 	 -with-report .github/data/test_output/nextflow_report.html \
  	 -with-trace .github/data/test_output/nextflow_trace.tsv
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -44,5 +44,5 @@ jobs:
       uses: actions/upload-artifact@v4
       if: always()
       with:
-        name: artifacts-BCCDC-PHL-tbprofiler-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }}
+        name: artifacts-BCCDC-PHL-routine-assembly-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }}
         path: artifacts
diff --git a/modules/prokka.nf b/modules/prokka.nf
@@ -4,7 +4,7 @@ process prokka {
 
     errorStrategy 'ignore'
 
-    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_prokka.{gbk,gff}", mode: 'copy'
+    publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy'
 
     input:
     tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode)