Update modules

CHANGELOG.md

@@ -12,11 +12,27 @@ 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`
 
+- [#518](https://github.com/nf-core/taxprofiler/pull/518) Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133)
+
 ### `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

@@ -97,6 +97,10 @@ While one can include both short-read and long-read data in one run, we recommen
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
+:::warning
+FASTA input will not go through any preprocessing steps, and will go directly to profiling.
+:::
+
 ### Full database sheet
 
 nf-core/taxprofiler supports multiple databases being classified/profiled against in parallel for each tool.
@@ -363,6 +367,8 @@ 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