Replace Bowtie2 custom modules with official nf-core ones

CHANGELOG.md

@@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#754](https://github.com/nf-core/mag/pull/754) - Replaced local module with nf-core module for all Bowtie2 processes (reported by @MeriamOs, fix by @jfy133)
+
 ### `Fixed`
 
+- [#754](https://github.com/nf-core/mag/pull/754) - Fix version reporting in binning preparation and ancient DNA workflows (fix by @jfy133)
+
 ### `Dependencies`
 
 ### `Deprecated`
@@ -33,8 +37,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#753](https://github.com/nf-core/mag/pull/753) - Fix iGenomes reference support for host removal reference genome (reported by @Thomieh73, fix by @jfy133)
 - [#759](https://github.com/nf-core/mag/pull/758) - Fixed parameters that allow both files or directories to not error with directories, and general file input validation improvements (reported by @mjfi2sb3, fix by @jfy133)
 
-### `Deprecated`
-
 ## 3.3.0 [2024-12-19]
 
 ### `Added`

conf/modules.config

@@ -347,24 +347,42 @@ process {
         ]
     }
 
+    withName: BOWTIE2_ASSEMBLY_BUILD {
+        ext.prefix = { "${meta.assembler}-${meta.id}" }
+    }
+
     withName: BOWTIE2_ASSEMBLY_ALIGN {
+        tag        = { "${meta.assembler}-${meta.id}-${meta3.id}" }
         ext.args   = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''
-        ext.prefix = { "${meta.id}.assembly" }
+        ext.args2  = ""
+        ext.prefix = { "${meta.assembler}-${meta.id}-${meta3.id}" }
         publishDir = [
             [
-                path: { "${params.outdir}/Assembly/${assembly_meta.assembler}/QC/${assembly_meta.id}" },
+                path: { "${params.outdir}/Assembly/${meta.assembler}/QC/${meta.id}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.log",
             ],
             [
-                path: { "${params.outdir}/Assembly/${assembly_meta.assembler}/QC/${assembly_meta.id}" },
+                path: { "${params.outdir}/Assembly/${meta.assembler}/QC/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{bam,bai}",
+                pattern: "*.{bam,csi}",
                 enabled: params.save_assembly_mapped_reads,
             ],
         ]
     }
 
+    withName: SAMTOOLS_INDEX {
+        ext.prefix = { "${meta.assembler}-${meta.id}-${meta3.id}" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/Assembly/${meta.assembler}/QC/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{bam}",
+                enabled: params.save_assembly_mapped_reads,
+            ]
+        ]
+    }
+
     withName: 'MAG_DEPTHS_PLOT|MAG_DEPTHS_SUMMARY' {
         publishDir = [path: { "${params.outdir}/GenomeBinning/depths/bins" }, mode: params.publish_dir_mode, pattern: "*.{png,tsv}"]
     }

modules.json

@@ -36,6 +36,16 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "bowtie2/align": {
+                        "branch": "master",
+                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
+                        "installed_by": ["modules"]
+                    },
+                    "bowtie2/build": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
@@ -267,6 +277,16 @@
                         "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
                         "installed_by": ["modules"]
                     },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/sort": {
+                        "branch": "master",
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/mergepe": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",