Replace Bowtie2 custom modules with official nf-core ones

CHANGELOG.md

@@ -9,13 +9,21 @@ 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)
+- [#754](https://github.com/nf-core/mag/pull/754) - Made filenames consistent for all bowtie2 assembly-aligning output (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)
 - [#769](https://github.com/nf-core/mag/pull/769) - Fix megahit not emitting correct filenames due to suboptimal arguments ordering (reported and fix by @IceGreb)
 - [#771](https://github.com/nf-core/mag/pull/771) - Fix misspecified checkm2 database parameter check (reported by @dpelegri and fix by @jfy133)
 
 ### `Dependencies`
 
+| Tool    | Previous version | New version |
+| ------- | ---------------- | ----------- |
+| Bowtie2 | 2.4.2            | 2.5.2       |
+
 ### `Deprecated`
 
 ## v3.3.1 - [2025-02-13]

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}"]
     }

docs/output.md

@@ -219,9 +219,9 @@ Trimmed (short) reads are assembled with both megahit and SPAdes. Hybrid assembl
   - `[sample/group].contigs.fa.gz`: Compressed metagenome assembly in fasta format
   - `[sample/group].log`: Log file
   - `QC/[sample/group]/`: Directory containing QUAST files and Bowtie2 mapping logs
-    - `MEGAHIT-[sample].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the sample that the metagenome was assembled from, only present if `--coassemble_group` is not set.
+    - `MEGAHIT-[sample]-[sampleToMap].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the sample that the metagenome was assembled from, only present if `--coassemble_group` is not set.
     - `MEGAHIT-[sample/group]-[sampleToMap].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the respective sample ("sampleToMap").
-    - `MEGAHIT-[sample].[bam/bai]`: Optionally saved BAM file of the Bowtie2 mapping of reads against the assembly.
+    - `MEGAHIT-[sample]-[sampleToMap].[bam/bai]`: Optionally saved BAM file of the Bowtie2 mapping of reads against the assembly.
 
 </details>
 
@@ -238,9 +238,9 @@ Trimmed (short) reads are assembled with both megahit and SPAdes. Hybrid assembl
   - `[sample/group].contigs.fa.gz`: Compressed assembled contigs in fasta format
   - `[sample/group].spades.log`: Log file
   - `QC/[sample/group]/`: Directory containing QUAST files and Bowtie2 mapping logs
-    - `SPAdes-[sample].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the sample that the metagenome was assembled from, only present if `--coassemble_group` is not set.
+    - `SPAdes-[sample]-[sampleToMap].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the sample that the metagenome was assembled from, only present if `--coassemble_group` is not set.
     - `SPAdes-[sample/group]-[sampleToMap].bowtie2.log`: Bowtie2 log file indicating how many reads have been mapped from the respective sample ("sampleToMap").
-    - `SPAdes-[sample].[bam/bai]`: Optionally saved BAM file of the Bowtie2 mapping of reads against the assembly.
+    - `SPAdes-[sample]-[sampleToMap].[bam/bai]`: Optionally saved BAM file of the Bowtie2 mapping of reads against the assembly.
 
 </details>
 

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",