update to samtools 1.20 (#5852)

* update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot <[email protected]>
nf-core · Jun 20, 2024 · 41a4135 · 41a4135
1 parent 13c7a1b
commit 41a4135
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Showing 3 changed files with 18 additions and 9 deletions.
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
@@ -4,4 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.16.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'biocontainers/samtools:1.16.1--h6899075_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,45a83c5f3dddbc5dcab30035169f7ce8"
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
                 ],
                 "fai": [
                     [
@@ -44,11 +44,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,45a83c5f3dddbc5dcab30035169f7ce8"
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
                 ]
             }
         ],
-        "timestamp": "2024-01-17T17:48:35.562918"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T13:22:34.14237"
     },
     "test_custom_getchromsizes_bgzip": {
         "content": [
@@ -78,7 +82,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,45a83c5f3dddbc5dcab30035169f7ce8"
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
                 ],
                 "fai": [
                     [
@@ -105,10 +109,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,45a83c5f3dddbc5dcab30035169f7ce8"
+                    "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
                 ]
             }
         ],
-        "timestamp": "2024-01-17T17:49:02.562311"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-20T13:23:06.241379"
     }
 }