Merge pull request #528 from nf-core/bb-minor-fixes

Additional minor fixes from @jfy133's review for bouncy basenji release

CHANGELOG.md

@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome complexity/coverage estimation with Nonpareil (added by @jfy133)
-- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets now require a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee)
+- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets can specify a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee)
 - [#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)
@@ -26,7 +26,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | bbmap         | 39.01            | 39.06       |
 | bowtie2       | 2.4.4            | 2.5.2       |
 | bracken       | 2.7              | 2.9         |
-| cat/fastq     | 8.30             |
 | diamond       | 2.0.15           | 2.1.8       |
 | ganon         | 1.5.1            | 2.0.0       |
 | kraken2       | 2.1.2            | 2.1.3       |
@@ -37,7 +36,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | motus/profile | 3.0.3            | 3.1.0       |
 | multiqc       | 1.21             | 1.24.1      |
 | samtools      | 1.17             | 1.20        |
-| untar         | 4.7              | 4.8         |
 
 ### `Deprecated`
 

README.md

@@ -73,7 +73,7 @@ Additionally, you will need a database sheet that looks as follows:
 
 `databases.csv`:
 
-```
+```csv
 tool,db_name,db_params,db_path
 kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
 metaphlan,db1,,/<path>/<to>/metaphlan/metaphlan_database/

subworkflows/local/profiling.nf

@@ -90,16 +90,16 @@ workflow PROFILING {
         }
         .branch { meta, reads, db_meta, db ->
             centrifuge: db_meta.tool == 'centrifuge'
-            diamond: db_meta.tool == 'diamond'
-            kaiju: db_meta.tool == 'kaiju'
-            kraken2: db_meta.tool == 'kraken2' || db_meta.tool == 'bracken' // to reuse the kraken module to produce the input data for bracken
+            diamond:    db_meta.tool == 'diamond'
+            kaiju:      db_meta.tool == 'kaiju'
+            kraken2:    db_meta.tool == 'kraken2' || db_meta.tool == 'bracken' // to reuse the kraken module to produce the input data for bracken
             krakenuniq: db_meta.tool == 'krakenuniq'
-            malt:    db_meta.tool == 'malt'
-            metaphlan: db_meta.tool == 'metaphlan'
-            motus: db_meta.tool == 'motus'
-            kmcp: db_meta.tool == 'kmcp'
-            ganon: db_meta.tool == 'ganon'
-            unknown: true
+            malt:       db_meta.tool == 'malt'
+            metaphlan:  db_meta.tool == 'metaphlan'
+            motus:      db_meta.tool == 'motus'
+            kmcp:       db_meta.tool == 'kmcp'
+            ganon:      db_meta.tool == 'ganon'
+            unknown:    true
         }
 
     /*