From f7787ea987afff7d423cc54266194998e4b7b650 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Thu, 24 Oct 2024 17:03:54 +0200
Subject: [PATCH] update subworkflow and module tests as well

---
 .../local/call_svs/tests/main.nf.test.snap    | 68 +++++++++----------
 .../tests/main.nf.test.snap                   | 20 +++---
 2 files changed, 44 insertions(+), 44 deletions(-)

diff --git a/subworkflows/local/call_svs/tests/main.nf.test.snap b/subworkflows/local/call_svs/tests/main.nf.test.snap
index d787c6c3..a98cd2c6 100644
--- a/subworkflows/local/call_svs/tests/main.nf.test.snap
+++ b/subworkflows/local/call_svs/tests/main.nf.test.snap
@@ -44,8 +44,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -89,8 +89,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -98,7 +98,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:44:23.698467142"
+        "timestamp": "2024-10-24T17:02:02.111203392"
     },
     "2 samples - [bam, bai], fasta, fai, [], [] - sniffles -stub": {
         "content": [
@@ -203,8 +203,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -248,8 +248,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -257,7 +257,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:44:09.06083732"
+        "timestamp": "2024-10-24T17:01:46.823258931"
     },
     "1 sample - [bam, bai], fasta, fai, [], [] - severus": {
         "content": [
@@ -325,9 +325,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -370,9 +370,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -380,7 +380,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:45:21.860327776"
+        "timestamp": "2024-10-24T17:03:01.122230307"
     },
     "1 sample - [bam, bai], fasta, fai, [], bed - severus": {
         "content": [
@@ -869,8 +869,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -914,8 +914,8 @@
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,589fd8607c7131f786d565deb2846f0c",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff"
+                    "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -923,7 +923,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:44:38.364811814"
+        "timestamp": "2024-10-24T17:02:16.765237677"
     },
     "1 sample - [bam, bai], fasta, fai, [], [] - severus -stub": {
         "content": [
@@ -969,9 +969,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -1014,9 +1014,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -1024,7 +1024,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:45:07.510780167"
+        "timestamp": "2024-10-24T17:02:46.632770301"
     },
     "1 sample - [bam, bai], fasta, fai, [], [] - sniffles": {
         "content": [
@@ -1132,19 +1132,19 @@
                 "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                 "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
                 "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
-                "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
                 "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
-                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81",
+                "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:45:51.452818836"
+        "timestamp": "2024-10-24T17:03:31.605140498"
     },
     "1 sample - [bam, bai], fasta, fai, bed, [] - severus -stub": {
         "content": [
@@ -1190,9 +1190,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ],
                 "ch_multisample_tbi": [
                     [
@@ -1235,9 +1235,9 @@
                     "versions.yml:md5,0c2f48bb23bdcc814171177730552a0b",
                     "versions.yml:md5,110bc7290a8aa06aea1c1fd2bad26324",
                     "versions.yml:md5,7090d52a64ab671fdb51c6af429628f4",
-                    "versions.yml:md5,a41129f62453d49bc1979c1a20551d7c",
                     "versions.yml:md5,ad7a1d3e0b9738f34f6f4cf8c7a5a7ff",
-                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f"
+                    "versions.yml:md5,dab46ec91d22db3eee78879773b88f1f",
+                    "versions.yml:md5,e3d7bb4a6f78fefdab18f93069e7db81"
                 ]
             }
         ],
@@ -1245,7 +1245,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T13:45:36.486860378"
+        "timestamp": "2024-10-24T17:03:15.955632046"
     },
     "2 samples - [bam, bai], fasta, fai, [], [] - severus": {
         "content": [
diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
index fc781a42..ccea5233 100644
--- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
+++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
@@ -617,12 +617,12 @@
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
@@ -703,12 +703,12 @@
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
@@ -720,7 +720,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-08T11:10:45.14685419"
+        "timestamp": "2024-10-24T17:29:06.951556756"
     },
     "2 samples - 2 bed, fasta, fai, bed, par_bed - stub": {
         "content": [
@@ -800,12 +800,12 @@
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
@@ -886,12 +886,12 @@
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
                     "versions.yml:md5,13101c9283d4a82e859574b0a981311c",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
-                    "versions.yml:md5,4cc3d41c069a8739916c98834c001f7a",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
+                    "versions.yml:md5,a942827df377a5077fe916c5b4a509b8",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
@@ -903,7 +903,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-08T11:10:58.271571777"
+        "timestamp": "2024-10-24T17:29:20.425210338"
     },
     "1 sample - 1 bed, fasta, fai, bed, [] - stub": {
         "content": [