Update modules

CHANGELOG.md

@@ -12,11 +12,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#505](https://github.com/nf-core/taxprofiler/pull/505) - Add small files to the file `tower.yml` (added by @LilyAnderssonLee)
 - [#508](https://github.com/nf-core/taxprofiler/pull/508) - Add `nanoq` as a filtering tool for nanopore reads (added by @LilyAnderssonLee)
 - [#511](https://github.com/nf-core/taxprofiler/pull/511) - Add `porechop_abi` as an alternative adapter removal tool for long reads nanopore data (added by @LilyAnderssonLee)
+- [#512](https://github.com/nf-core/taxprofiler/pull/512) - Update all tools to the latest version and include nf-test (Updated by @LilyAnderssonLee & @jfy133)
 
 ### `Fixed`
 
 ### `Dependencies`
 
+| Tool      | Previous version | New version |
+| --------- | ---------------- | ----------- |
+| bbmap     | 39.01            | 39.06       |
+| bowtie2   | 2.4.4            | 2.5.2       |
+| bracken   | 2.7              | 2.9         |
+| diamond   | 2.0.15           | 2.1.8       |
+| ganon     | 1.5.1            | 2.0.0       |
+| kraken2   | 2.1.2            | 2.1.3       |
+| minimap2  | 2.24             | 2.28        |
+| samtools  | 1.17             | 1.20        |
+| megan     | 6.24.20          | 6.25.9      |
+| metaphlan | 4.0.6            | 4.1.1       |
+
 ### `Deprecated`
 
 ## v1.1.8 - Augmented Akita Patch [2024-06-20]

assets/multiqc_config.yml

@@ -33,6 +33,8 @@ report_section_order:
     order: 200
   filtlong:
     order: 100
+  nanoq:
+    order: 95
   bowtie2:
     order: 90
   samtools:
@@ -68,6 +70,7 @@ run_modules:
   - prinseqplusplus
   - porechop
   - filtlong
+  - nanoq
   - bowtie2
   - minimap2
   - samtools
@@ -206,6 +209,8 @@ table_columns_placement:
     Middle Split Percent: 560
   Filtlong:
     Target bases: 600
+  nanoq:
+    Read N50: 700
   BBDuk:
     Input reads: 800
     Total Removed bases percent: 810
@@ -305,6 +310,8 @@ table_columns_visible:
     Middle Split Percent: True
   Filtlong:
     Target bases: True
+  nanoq:
+    ReadN50: True
   BBDuk:
     Input reads: False
     Total Removed bases Percent: False

conf/modules.config

@@ -813,7 +813,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/ganon/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{tre,rep,lca,all,unc}'
+            pattern: '*.{tre,rep,lca,all,unc,log}'
         ]
     }
 

docs/usage.md

@@ -363,6 +363,8 @@ Centrifuge currently does not accept FASTA files as input, therefore no output w
 
 ##### DIAMOND
 
+DIAMOND can only accept a single input read file. To run DIAMOND on paired-end reads, please merge the reads (e.g., using `--shortread_qc_mergepairs`).
+
 DIAMOND only allows output of a single file format at a time, therefore parameters such `--diamond_save_reads` supplied will result in only aligned reads in SAM format will be produced, no taxonomic profiles will be available. Be aware of this when setting up your pipeline runs, depending on your particular use case.
 
 ##### Kaiju