Merge pull request #379 from hkaspersen/bracken_output_report_fix

Bracken output report addition
nf-core · Oct 1, 2023 · bd56d37 · bd56d37
2 parents 84752d0 + e6c2cf9
commit bd56d37
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Showing 6 changed files with 11 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#379](https://github.com/nf-core/taxprofiler/pull/379) Added support for previously missing Bracken-corrected Kraken2 report as output (added by @hkaspersen & @jfy133 )
 - [#380](https://github.com/nf-core/taxprofiler/pull/380) Updated to nf-core pipeline template v2.10 (added by @LilyAnderssonLee & @sofstam)
 
 ### `Fixed`

diff --git a/conf/modules.config b/conf/modules.config
@@ -471,8 +471,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/bracken/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.tsv'
-        ]
+            pattern: '*{.tsv,.txt}'
+    ]
     }
 
     withName: BRACKEN_COMBINEBRACKENOUTPUTS {

diff --git a/docs/output.md b/docs/output.md
@@ -345,6 +345,7 @@ The first step of using Bracken requires running Kraken2, therefore the initial
     - `bracken_<db_name>_combined_reports.txt`: combined bracken results as output from Bracken's `combine_bracken_outputs.py` script
     - `<db_name>/`
       - `<sample>_<db_name>.tsv`: TSV file containing per-sample summary of Bracken results with abundance information
+      - `<sample>_<db_name>.report_bracken_species.txt`: Kraken2 style report with Bracken abundance information
 
 </details>
 

diff --git a/modules.json b/modules.json
@@ -27,7 +27,7 @@
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "093e35505936bce5127e1d14966b6cac91cd137f",
                         "installed_by": ["modules"]
                     },
                     "bracken/combinebrackenoutputs": {

diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf
diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml