add window test

tests/modules/mosdepth/main.nf

@@ -2,8 +2,9 @@
 
 nextflow.enable.dsl = 2
 
-include { MOSDEPTH                  } from '../../../modules/mosdepth/main.nf'
-include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH                    } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_FAIL   } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf'
 
 workflow test_mosdepth {
     input  = [
@@ -49,6 +50,17 @@ workflow test_mosdepth_cram_bed {
     MOSDEPTH ( input, bed, fasta )
 }
 
+workflow test_mosdepth_window {
+    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_WINDOW ( input, [], [] )
+}
+
 workflow test_mosdepth_fail {
     input  = [
                 [ id:'test', single_end:true ],

tests/modules/mosdepth/nextflow.config

@@ -4,4 +4,7 @@ process {
     withName: MOSDEPTH_FAIL {
         ext.args = "--by 100"
     }
+    withName: MOSDEPTH_WINDOW {
+        ext.args = "--by 100"
+    }
 }

tests/modules/mosdepth/test.yml

@@ -66,6 +66,26 @@
     - path: output/mosdepth/test.regions.bed.gz.csi
       md5sum: 47669cfe41f3e222e74d81e1b1be191f
 
+- name: mosdepth test_mosdepth_window
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: 39e0e707ec32feb5176fd20a95f1f468
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: f02e2cb49cc050e13d76942d6960827a
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 257d67678136963d9dd904330079609d
+
 - 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: