Update CENTRIFUGE module and not by default generate SAM alignments

nf-core · Jul 27, 2023 · 9f98ccd · 9f98ccd
1 parent 4627208
commit 9f98ccd
Show file tree

Hide file tree

Showing 6 changed files with 14 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -45,6 +45,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
+- [#335](https://github.com/nf-core/taxprofiler/pull/335) Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, to due Centrifuge bug modifying profile header. SAM alignments can still be generated if `--out-fmt` supplied in `database.csv` (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
+
 ## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
 
 ### `Added`

diff --git a/conf/modules.config b/conf/modules.config
@@ -559,7 +559,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{txt,sam,gz}'
+            pattern: '*.{txt,sam,tab,gz}'
         ]
     }
 

diff --git a/modules.json b/modules.json
@@ -42,7 +42,7 @@
                     },
                     "centrifuge/centrifuge": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "7b0b4276fbad744a69c35d3cbf9d55fdfc9491bd",
                         "installed_by": ["modules"]
                     },
                     "centrifuge/kreport": {

diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -230,7 +230,7 @@ workflow PROFILING {
                                         db: it[3]
                                 }
 
-        CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads  )
+        CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads  )
         ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )