add must fail test

modules/mosdepth/main.nf

@@ -31,7 +31,7 @@ process MOSDEPTH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--fasta ${fasta}" : ""
     def interval = bed ? "--by ${bed}" : ""
-    if (bed && ext.args.contains("--by")) {
+    if (bed && args.contains("--by")) {
         exit 1, "--by can only be specified once."
     }
 

tests/modules/mosdepth/main.nf

@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH                  } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf'
 
 workflow test_mosdepth {
     input  = [
@@ -47,3 +48,14 @@ workflow test_mosdepth_cram_bed {
 
     MOSDEPTH ( input, bed, fasta )
 }
+
+workflow test_mosdepth_fail {
+    input  = [
+                [ id:'test', single_end:true ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+            ]
+    bed  = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+
+    MOSDEPTH_FAIL ( input, bed, [] )
+}

tests/modules/mosdepth/nextflow.config

@@ -1,5 +1,7 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: MOSDEPTH_FAIL {
+        ext.args = "--by 100"
+    }
 }

tests/modules/mosdepth/test.yml

@@ -65,3 +65,9 @@
       md5sum: 5d398caf7171ec4406278e2add3009ae
     - path: output/mosdepth/test.regions.bed.gz.csi
       md5sum: 47669cfe41f3e222e74d81e1b1be191f
+
+- name: mosdepth test_mosdepth_fail
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  exitcode: 1