From 33b76c2d14bc02d252f2ba452772bedee718e799 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 Dec 2024 13:38:01 +0100
Subject: [PATCH] bump ngsbits

---
 modules/nf-core/ngsbits/samplegender/environment.yml   |  2 +-
 modules/nf-core/ngsbits/samplegender/main.nf           |  6 +++---
 modules/nf-core/ngsbits/samplegender/meta.yml          |  2 +-
 .../nf-core/ngsbits/samplegender/tests/main.nf.test    |  2 +-
 .../ngsbits/samplegender/tests/main.nf.test.snap       | 10 +++++-----
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml
index 932d1556a7a..98be7c334ec 100644
--- a/modules/nf-core/ngsbits/samplegender/environment.yml
+++ b/modules/nf-core/ngsbits/samplegender/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ngs-bits=2023_02
+  - bioconda::ngs-bits=2024_11
diff --git a/modules/nf-core/ngsbits/samplegender/main.nf b/modules/nf-core/ngsbits/samplegender/main.nf
index 3562238dfcd..6551490845c 100644
--- a/modules/nf-core/ngsbits/samplegender/main.nf
+++ b/modules/nf-core/ngsbits/samplegender/main.nf
@@ -4,13 +4,13 @@ process NGSBITS_SAMPLEGENDER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ngs-bits:2023_02--py311ha0b7adc_2':
-        'biocontainers/ngs-bits:2023_02--py311ha0b7adc_2' }"
+        'https://depot.galaxyproject.org/singularity/ngs-bits:2024_11--py312hd80e9a6_0':
+        'biocontainers/ngs-bits:2024_11--py312hd80e9a6_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
     tuple val(meta2), path(fasta)
-    tuple val(meta2), path(fai)
+    tuple val(meta3), path(fai)
     val method
 
     output:
diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml
index 54a611812df..fd5a55024c2 100644
--- a/modules/nf-core/ngsbits/samplegender/meta.yml
+++ b/modules/nf-core/ngsbits/samplegender/meta.yml
@@ -36,7 +36,7 @@ input:
         type: file
         description: The reference FASTA to use (mandatory when CRAM files are used)
         pattern: "*.{fasta,fa,fna}"
-  - - meta2:
+  - - meta3:
         type: map
         description: |
           Groovy Map containing reference fasta information
diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test
index 4f8379b4022..0917b7ddeed 100644
--- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test
+++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test
@@ -9,7 +9,7 @@ nextflow_process {
     tag "ngsbits"
     tag "ngsbits/samplegender"
 
-    // Only a stub test here because the modules needs the full chrX and chrY
+    // Only a stub test here because the module needs the full chrX and chrY
     test("homo_sapiens - bam, bai, [], [], sry - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
index 48fd8af9c12..cb493a2c25b 100644
--- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
+++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b"
+                    "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333"
                 ],
                 "tsv": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b"
+                    "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-03-18T15:36:37.639882564"
+        "timestamp": "2024-12-10T13:36:08.650020628"
     }
 }
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