From d014d32ea2b3d79a5c3735fe9a8b26243a27a834 Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Thu, 16 May 2024 09:06:27 -0700
Subject: [PATCH] Fix publishing prokka outputs (#51)

* Fix publishDir pattern for prokka outputs

* Run prokka in tests

* Fix artifacts name
---
 .github/scripts/run_pipeline.sh | 1 +
 .github/workflows/tests.yml     | 2 +-
 modules/prokka.nf               | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
index 7cc5112..486bb6b 100755
--- a/.github/scripts/run_pipeline.sh
+++ b/.github/scripts/run_pipeline.sh
@@ -10,5 +10,6 @@ nextflow run main.nf \
 	 --cache ${HOME}/.conda/envs \
 	 --fastq_input .github/data/fastq \
 	 --outdir .github/data/test_output \
+	 --prokka \
 	 -with-report .github/data/test_output/nextflow_report.html \
  	 -with-trace .github/data/test_output/nextflow_trace.tsv
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f5471f0..b4a7ccf 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -44,5 +44,5 @@ jobs:
       uses: actions/upload-artifact@v4
       if: always()
       with:
-        name: artifacts-BCCDC-PHL-tbprofiler-nf-nextflow-v${{ 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
index f4a779c..5d429a7 100644
--- 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)