Fix artifacts path

.github/scripts/install_conda.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -eo pipefail
 
-artifacts_dir="artifacts-nextflow-${NXF_VER}"
+artifacts_dir="artifacts"
 
 echo "Install Miniconda .." >> ${artifacts_dir}/test.log
 

.github/scripts/install_nextflow.sh

@@ -2,7 +2,7 @@
 
 set -eo pipefail
 
-artifacts_dir="artifacts-nextflow-${NXF_VER}"
+artifacts_dir="artifacts"
 
 echo Install Nextflow .. >> ${artifacts_dir}/test.log
 

.github/scripts/prepare_artifacts.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-artifacts_dir="artifacts-nextflow-${NXF_VER}"
+artifacts_dir="artifacts"
 
 echo "Prepare artifacts .." >> ${artifacts_dir}/test.log
 

.github/scripts/run_pipeline.sh

@@ -4,8 +4,6 @@ set -eo pipefail
 
 sed -i 's/cpus = 8/cpus = 4/g' nextflow.config 
 
-cat nextflow.config
-
 nextflow run main.nf \
 	 -profile conda \
 	 --cache ${HOME}/.conda/envs \

.github/workflows/pull_request.yml

@@ -43,5 +43,5 @@ jobs:
       env:
         NXF_VER: ${{ matrix.nextflow_version }}
       with:
-        name: artifacts-nextflow-${{ matrix.nextflow_version }}
-        path: artifacts-nextflow-${NXF_VER}
+        name: artifacts-nextflow-${{ matrix.nextflow_version }}-${{ env.RUN_UNIQUE_ID }}
+        path: artifacts

nextflow.config

@@ -52,6 +52,7 @@ def parsePipelineName(name) {
 
 profiles {
     conda {
+	conda.enabled = true
 	process.conda = "$baseDir/environments/environment.yml"
 	if (params.cache){
 	    conda.cacheDir = params.cache
@@ -64,3 +65,9 @@ process {
 	cpus = 8
     }
 }
+
+trace {
+    enabled = true
+    overwrite = true
+    file = "${params.outdir}/nextflow_trace.tsv"
+}