fix: tests

nf-core · May 30, 2021 · 4fbbf80 · 4fbbf80
1 parent 77a5c65
commit 4fbbf80
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/modules/nf-core/software/gatk4/markduplicates/main.nf b/modules/nf-core/software/gatk4/markduplicates/main.nf
@@ -7,8 +7,9 @@ options        = initOptions(params.options)
 process GATK4_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_low'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

diff --git a/tests/subworkflows/local/markduplicates/main.nf b/tests/subworkflows/local/markduplicates/main.nf
@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 // Don't overwrite global params.modules, create a copy instead and use that within the main script.
 def modules = params.modules.clone()
 
-include { MARKDUPLICATES } from '../../../../subworkflow/local/markduplicates' addParams(
+include { MARKDUPLICATES } from '../../../../subworkflows/local/markduplicates' addParams(
     markduplicates_options: modules['markduplicates']
 )