Add nf-test: test_falcobbduk

CHANGELOG.md

@@ -8,13 +8,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#559](https://github.com/nf-core/taxprofiler/pull/559) Profiling of long reads with motus (added by @LilyAnderssonLee and @sofstam )
+- [#591](https://github.com/nf-core/taxprofiler/pull/591) Add options to enable the `abi` option to predict adapters or provide a custom adapter list for `porechop_abi` (❤️ to @AlexHoratio for suggesting, fix by @LilyAnderssonLee and @sofstam)
 - [#595](https://github.com/nf-core/taxprofiler/pull/595) **New classifier** [sylph](https://github.com/bluenote-1577/sylph) (added by @sofstam)
 - [#608](https://github.com/nf-core/taxprofiler/pull/608) **New classifier** [melon](https://github.com/xinehc/melon) (added by @parisis and @sofstam)
+- [#694](https://github.com/nf-core/taxprofiler/pull/694) Developer and contributor documentation (by @jfy133)
+- [#698](https://github.com/nf-core/taxprofiler/pull/698) Add new config and nf-test for `test_falcobbduk` (by @jfy133)
+-
 
 ### `Fixed`
 
 ### `Changed`
 
+- [#696](https://github.com/nf-core/taxprofiler/pull/696) Switch Slack channel reporting to nf-slack plugin for AWS Megatests (by @jfy133)
+
 ### `Dependencies`
 
 | Tool | Previous version | New version |
@@ -23,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
+- [#698](https://github.com/nf-core/taxprofiler/pull/698) Deprecate `test_bbduk` and `test_falco` test profiles (merged into `test_falcobduk) (by @jfy133)
 - [#696](https://github.com/nf-core/taxprofiler/pull/696) Remove hook_url from the pipeline configuration, cf[tools#4051](https://github.com/nf-core/tools/pull/4051) (by @jfy133 and @FriederikeHanssen)
 
 ## v1.2.6 - [2026-02-16]
@@ -120,8 +127,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#576](https://github.com/nf-core/taxprofiler/pull/576) Sort input to krakenuniq to enable retrieval of cached batch tasks (❤️ to @muniheart for reporting and fix)
 - [#569](https://github.com/nf-core/taxprofiler/pull/569) Updated to nf-core pipeline template v3.1.2 (added by @sofstam)
 - [#571](https://github.com/nf-core/taxprofiler/pull/571) Updated to nf-core pipeline template v3.2.0 (added by @sofstam)
-- [#591](https://github.com/nf-core/taxprofiler/pull/591) Add options to enable the `abi` option to predict adapters or provide a custom adapter list for `porechop_abi` (❤️ to @AlexHoratio
-  for suggesting, fix by @LilyAnderssonLee and @sofstam)
 
 ### `Fixed`
 

conf/test_bbduk.config → conf/test_falcobbduk.config

@@ -1,13 +1,13 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/taxprofiler -profile test_bbduk,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_falcobbduk,<docker/singularity> --outdir <OUTDIR>
 
-----------------------------------------------------------------------------------------
+---------------------------------------------------------------------------------------------------------
 */
 
 process {
@@ -20,18 +20,20 @@ process {
 }
 
 params {
-    config_profile_name                = 'Test profile for bbduk'
-    config_profile_description         = "Minimal test to check the default tool of short-read complexity filtering, bbduk"
+    config_profile_name                = 'Test profile for falco and bbduk'
+    config_profile_description         = "Minimal test to falco and bbduk functionality in the short-read preprocessing steps"
 
     // Input data
-    input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
+    input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_shortreadfastqpairsonly.csv'
     databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.3.csv'
+    preprocessing_qc_tool              = 'falco'
     perform_shortread_qc               = true
-    perform_longread_qc                = true
+    perform_longread_qc                = false
     perform_shortread_complexityfilter = true
     shortread_complexityfilter_tool    = 'bbduk'
+    save_complexityfiltered_reads      = true
     perform_shortread_hostremoval      = true
-    perform_longread_hostremoval       = true
+    perform_longread_hostremoval       = false
     perform_runmerging                 = true
     hostremoval_reference              = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                          = true

nextflow.config

@@ -349,17 +349,14 @@ profiles {
     test_malt {
         includeConfig 'conf/test_malt.config'
     }
-    test_falco {
-        includeConfig 'conf/test_falco.config'
-    }
     test_fastp {
         includeConfig 'conf/test_fastp.config'
     }
     test_alternativepreprocessing {
         includeConfig 'conf/test_alternativepreprocessing.config'
     }
-    test_bbduk {
-        includeConfig 'conf/test_bbduk.config'
+    test_falcobbduk {
+        includeConfig 'conf/test_falcobbduk.config'
     }
     test_prinseqplusplus {
         includeConfig 'conf/test_prinseqplusplus.config'

tests/.nftignore

@@ -1,7 +1,9 @@
 .DS_Store
 bbduk/*.log
+bbduk/*.fastq.gz
 centrifuge/*.{fastq.gz,txt}
 diamond/*/*.{tsv,log}
+falco/*/*{_fastqc_data.txt,_report.html}
 fastp/*.{html,zip,json,log}
 fastqc/*_fastqc.{html,zip}
 fastqc/*/*fastqc.zip