Merge branch 'dev' into jfy133-review-fixes

nf-core · Sep 25, 2024 · 0c647d1 · 0c647d1
2 parents b9e3c38 + 0f5651f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#523](https://github.com/nf-core/taxprofiler/pull/523) Removed hardcoded `-m lca` from GANON_CLASSIFY due to more options in new version of ganon (fixed by @LilyAnderssonLee & @jfy133)
 - [#531](https://github.com/nf-core/taxprofiler/pull/531) Fix FASTA input validation in schema allowing FASTQ extension, expand allowed FASTA extensions (fixed by @jfy133)
 - [#512](https://github.com/nf-core/taxprofiler/pull/532) Minor formatting and ordering improvements in MultiQC report (by @jfy133)
+- [#532](https://github.com/nf-core/taxprofiler/pull/532) - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133)
 
 ### `Dependencies`
 

diff --git a/docs/usage/faq-troubleshooting.md b/docs/usage/faq-troubleshooting.md
@@ -1,9 +1,31 @@
 # Troubleshooting and FAQs
 
-## I get a warning during centrifuge_kreport process with exit status 255
+## I get a warning during CENTRIFUGE_KREPORT or KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE process with exit status 255
 
 When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.
 
-When trying to convert this to a kraken-style report, the conversion tool will exit with a status code `255`, and provide a `WARN`.
+When trying to convert this to a kraken-style report or merging together, the tools will exit with a status code `255`, and provide a `WARN`.
 
-This is _not_ an error nor a failure of the pipeline, just your sample has no hits to the provided database when using centrifuge.
+This is _not_ an error nor a failure of the pipeline, just your sample has no hits to the provided database when using Centrifuge.
+
+## Why does any error or failed process from BRACKEN_BRACKEN get ignored?
+
+If Kraken2 doesn't classify any reads (100% unclassified) Bracken will fail on that input.
+Having no reads taxonomically classified can be a reasonable outcome for some samples, and we don't want to treat this as an error.
+
+Therefore to allow the remainder of a given run to complete if a single Bracken task fails, [we set the Nextflow `errorStrategy` to `ignore`](https://github.com/nf-core/taxprofiler/blob/5d3ee5513a84f92773c8376c55b5f4da39835307/conf/base.config#L61-L63).
+You will still get a warning in the Nextflow console output and log that a Bracken task failed.
+
+If you want to change this behaviour, you can override the `errorStrategy` in your own Nextflow configuration file.
+
+For example:
+
+```nextflow
+process {
+    withName: BRACKEN_BRACKEN {
+        errorStrategy = 'retry'
+    }
+}
+```
+
+Other `errorStrategy` options can be found on the [Nextflow documentation](https://www.nextflow.io/docs/latest/process.html#errorstrategy).
diff --git a/nextflow.config b/nextflow.config
@@ -314,20 +314,19 @@ profiles {
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
-    test                    { includeConfig 'conf/test.config'      }
-    test_full               { includeConfig 'conf/test_full.config' }
-    test_noprofiling        { includeConfig 'conf/test_noprofiling.config' }
-    test_nopreprocessing    { includeConfig 'conf/test_nopreprocessing.config' }
-    test_nothing            { includeConfig 'conf/test_nothing.config' }
-    test_motus              { includeConfig 'conf/test_motus.config' }
-    test_krakenuniq         { includeConfig 'conf/test_krakenuniq.config' }
-    test_malt               { includeConfig 'conf/test_malt.config' }
-    test_falco              { includeConfig 'conf/test_falco.config' }
-    test_fastp              { includeConfig 'conf/test_fastp.config' }
+    test                                 { includeConfig 'conf/test.config'                          }
+    test_full                            { includeConfig 'conf/test_full.config'                     }
+    test_noprofiling                     { includeConfig 'conf/test_noprofiling.config'              }
+    test_nopreprocessing                 { includeConfig 'conf/test_nopreprocessing.config'          }
+    test_nothing                         { includeConfig 'conf/test_nothing.config'                  }
+    test_motus                           { includeConfig 'conf/test_motus.config'                    }
+    test_krakenuniq                      { includeConfig 'conf/test_krakenuniq.config'               }
+    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_prinseqplusplus    { includeConfig 'conf/test_prinseqplusplus.config' }
-
+    test_bbduk                           { includeConfig 'conf/test_bbduk.config'                    }
+    test_prinseqplusplus                 { includeConfig 'conf/test_prinseqplusplus.config'          }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
@@ -39,7 +39,6 @@ workflow LONGREAD_PREPROCESSING {
         FASTQC_PROCESSED ( ch_processed_reads )
         ch_versions      = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
-
     } else if (params.preprocessing_qc_tool == 'falco') {
         FALCO_PROCESSED ( ch_processed_reads )
         ch_versions      = ch_versions.mix( FALCO_PROCESSED.out.versions )

diff --git a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf b/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf
@@ -211,7 +211,7 @@ def toolCitationText() {
         "Long read preprocessing was performed with:",
         params.longread_adapterremoval_tool == "porechop_abi" ? "Porechop_ABI (Bonenfant et al. 2023)," : "",
         params.longread_adapterremoval_tool == "porechop" ? "Porechop (Wick et al. 2017)," : "",
-        params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)," : "",
+        params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)." : "",
         params.longread_filter_tool == "nanoq" ? "Nanoq (Steinig and Coin 2022)." : "",
     ].join(' ').trim()