Merge pull request #421 from nf-core/fix-krakenuniq

Fix krakenuniq reads output

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### `Fixed`
+
+- [#421](https://github.com/nf-core/taxprofiler/pull/421) Updated the krakenuniq/preloadedkrakenuniq module that contained a fix for saving the output reads (❤️ to @SannaAb for reporting, fix by @Midnighter)
+
 ## v1.1.2 - Augmented Akita Patch [2023-10-27]
 
 ### `Added`

conf/modules.config

@@ -500,7 +500,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{txt,fastq.gz}'
+            pattern: '*.{txt,fasta.gz}'
         ]
     }
 

docs/output.md

@@ -375,23 +375,23 @@ You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply
 
 ### KrakenUniq
 
-[KrakenUniq](https://github.com/fbreitwieser/krakenuniq) (formerly KrakenHLL) is an extenson to the fast k-mer-based classification [Kraken](https://github.com/DerrickWood/kraken) with an efficient algorithm for additionally assessing the coverage of unique k-mers found in each species in a dataset.
+[KrakenUniq](https://github.com/fbreitwieser/krakenuniq) (formerly KrakenHLL) is an extension to the fast k-mer-based classification performed by [Kraken](https://github.com/DerrickWood/kraken) with an efficient algorithm for additionally assessing the coverage of unique k-mers found in each species in a dataset.
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `krakenuniq/`
   - `<db_name>/`
-    - `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample
-    - `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample
-    - `<sample_id>_<db_name>.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits
-    - `<sample_id>_<db_name>.classifiedreads.txt`: A list of read IDs and the hits each read had against each database for a given sample
+    - `<sample_id>_<db_name>[.merged].classified.fasta.gz`: Optional FASTA file containing all reads that had a hit against a reference in the database for a given sample. Paired-end input reads are merged in this output.
+    - `<sample_id>_<db_name>[.merged].unclassified.fasta.gz`: Optional FASTA file containing all reads that did not have a hit in the database for a given sample. Paired-end input reads are merged in this output.
+    - `<sample_id>_<db_name>.krakenuniq.report.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits.
+    - `<sample_id>_<db_name>.krakenuniq.classified.txt`: An optional list of read IDs and the hits each read had against each database for a given sample.
 
 </details>
 
-The main taxonomic classification file from KrakenUniq is the `*report.txt` file. This is an extension of the Kraken2 report with the additional k-mer coverage information that provides more information about the accuracy of hits.
+The main taxonomic classification file from KrakenUniq is the `*.krakenuniq.report.txt` file. This is an extension of the Kraken2 report with the additional k-mer coverage information that provides more information about the accuracy of hits.
 
-You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply `--krakenuniq_save_reads` and/or `--krakenuniq_save_readclassification` parameters to the pipeline.
+You will only receive the `.fasta.gz` and `*.krakenuniq.classified.txt` file if you supply `--krakenuniq_save_reads` and/or `--krakenuniq_save_readclassification` parameters to the pipeline.
 
 :::info
 The output system of KrakenUniq can result in other `stdout` or `stderr` logging information being saved in the report file, therefore you must check your report files before downstream use!

modules.json

@@ -143,7 +143,7 @@
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "451df5258e0c03cb4e835bb02c22a9a31b44eb0d",
+                        "git_sha": "8bbaa881ab9e59f3e18680550d65d52339640630",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {