From 8381a5e5dd73228b3fe744e51f1964d62c28c1e5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 24 May 2022 14:43:40 +0200
Subject: [PATCH] add window test

---
 tests/modules/mosdepth/main.nf         | 16 ++++++++++++++--
 tests/modules/mosdepth/nextflow.config |  3 +++
 tests/modules/mosdepth/test.yml        | 20 ++++++++++++++++++++
 3 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf
index eab47e89..96a9ef20 100644
--- a/tests/modules/mosdepth/main.nf
+++ b/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 ],
diff --git a/tests/modules/mosdepth/nextflow.config b/tests/modules/mosdepth/nextflow.config
index 85674a3c..4a6153e6 100644
--- a/tests/modules/mosdepth/nextflow.config
+++ b/tests/modules/mosdepth/nextflow.config
@@ -4,4 +4,7 @@ process {
     withName: MOSDEPTH_FAIL {
         ext.args = "--by 100"
     }
+    withName: MOSDEPTH_WINDOW {
+        ext.args = "--by 100"
+    }
 }
diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml
index a927396c..a3115d6e 100644
--- a/tests/modules/mosdepth/test.yml
+++ b/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: