Use nf-tests for checkQC

modules/nf-core/checkqc/main.nf

@@ -1,6 +1,6 @@
 process CHECKQC {
     label 'process_low'
-    stageInMode 'copy'
+    errorStrategy 'ignore'
 
     conda "bioconda::checkqc=3.6.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/checkqc/tests/main.nf.test

@@ -0,0 +1,40 @@
+nextflow_process {
+
+    name "Test Process CHECKQC"
+    script "modules/nf-core/checkqc/main.nf"
+    process "CHECKQC"
+    tag "checkqc"
+    tag "modules"
+    tag "modules_nfcore"
+
+    test("Run checkqc without error") {
+        config "./test_checkqc.config"
+
+        setup {
+            run("UNTAR") {
+                script "modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([ [], file(params.test_data['homo_sapiens']['illumina']['test_interop_bcl2fastqstats_flowcell'], checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = UNTAR.out.untar.map{ it[1] }
+                    input[1] = []
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

modules/nf-core/checkqc/tests/tags.yml

@@ -0,0 +1,2 @@
+checkqc:
+  - modules/nf-core/checkqc/**

tests/modules/nf-core/checkqc/nextflow.config → modules/nf-core/checkqc/tests/test_checkqc.config

@@ -1,5 +1,8 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+
+    withName: CHECKQC {
+        ext.args = '--downgrade-errors ReadsPerSampleHandler'
+    }
 }

tests/config/pytest_modules.yml

@@ -708,10 +708,6 @@ checkm/qa:
   - modules/nf-core/checkm/qa/**
   - tests/modules/nf-core/checkm/qa/**
 
-checkqc:
-  - modules/nf-core/checkqc/**
-  - tests/modules/nf-core/checkqc/**
-
 checkv/downloaddatabase:
   - modules/nf-core/checkv/downloaddatabase/**
   - tests/modules/nf-core/checkv/downloaddatabase/**

tests/config/test_data.config

@@ -490,6 +490,8 @@ params {
 
                 varlociraptor_scenario                                  = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml"
 
+                test_interop_bcl2fastqstats_flowcell                    = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/interop_bcl2fastqstats/test_flowcell_stats.tar.gz"
+
                 contig_ploidy_priors_table                              = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
 
                 purecn_ex1_bam                                          = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam"