Update nf-core modules (#486)

* Update nf-core modules * fix tests * update methylation config * update test * update modules * update tests
genomic-medicine-sweden · Nov 6, 2024 · 73cca58 · 73cca58
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -127,16 +127,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Module updates
 
-| Tool       | Old version | New version |
-| ---------- | ----------- | ----------- |
-| fqcrs      | 0.1.0       |
-| severus    |             | 1.1         |
-| longphase  |             | 1.7.3       |
-| genmod     | 3.8.2       | 3.9         |
-| WhatsHap   | 2.2         | 2.3         |
-| SVDB       |             | 2.8.1       |
-| hifiasm    | 0.19.8      | 0.20.0      |
-| HiFiCNV    | 0.1.7       | 1.0.0       |
+| Tool           | Old version | New version |
+| -------------- | ----------- | ----------- |
+| fqcrs          | 0.1.0       |
+| severus        |             | 1.1         |
+| longphase      |             | 1.7.3       |
+| genmod         | 3.8.2       | 3.9         |
+| WhatsHap       | 2.2         | 2.3         |
+| SVDB           |             | 2.8.1       |
+| hifiasm        | 0.19.8      | 0.20.0      |
+| HiFiCNV        | 0.1.7       | 1.0.0       |
+| samtools/faidx | 1.2         | 1.21        |
+| samtools/index | 1.2         | 1.21        |
+| samtools/merge | 1.2         | 1.21        |
+| stranger       | 0.9.1       | 0.9.2       |
+| multiqc        | 1.21        | 1.25.1      |
 
 > [!NOTE]
 > Version has been updated if both old and new version information is present.

diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
@@ -34,7 +34,7 @@ process {
     }
 
 
-    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT' {
+    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
         ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" }
         ext.args = { [
             "--sample_name=${meta.id}",

diff --git a/modules.json b/modules.json
diff --git a/modules/local/create_pedigree_file/tests/main.nf.test.snap b/modules/local/create_pedigree_file/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                 "family\tHG002.Revio\t0\t0\t0\t2"
             ],
             [
-                "versions.yml:md5,c0d2b2d33f1c465351d65e149ae88f0c"
+                "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-12T10:24:34.60478278"
+        "timestamp": "2024-11-04T16:16:12.293913485"
     },
     "create_pedigree_file - multiple samples": {
         "content": [
@@ -25,13 +25,13 @@
                 "FAM2\tHG002_Revio_AB\t0\t0\t0\t1"
             ],
             [
-                "versions.yml:md5,c0d2b2d33f1c465351d65e149ae88f0c"
+                "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-12T10:40:54.71628575"
+        "timestamp": "2024-11-04T16:16:19.916570689"
     }
 }
diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff
diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml
diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml