nf-core · jfy133 · Mar 6, 2025 · Jan 15, 2025 · Mar 3, 2025 · Mar 3, 2025
@@ -123,6 +123,7 @@ We thank the following people for their contributions to the development of this
 - [Jianhong Ou](https://github.com/jianhong)
 - [Rafal Stepien](https://github.com/rafalstepien)
 - [Mahwash Jamy](https://github.com/mjamy)
+- [Alex Caswell](https://github.com/AlexHoratio)
 
 ### Acknowledgments
 

@@ -401,7 +401,7 @@ This is the last possible preprocessing step, so if you have multiple runs or li
 
 Note that you will only find samples that went through the run merging step in this directory. For samples that had a single run or library will not go through this step of the pipeline and thus will not be present in this directory.
 
-This directory and its FASTQ files will only be present if you supply `--save_runmerged_reads`.Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
+This directory and its FASTQ files will only be present if you supply `--save_runmerged_reads`. Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
 
 ### Bracken
 

@@ -59,7 +59,7 @@ tar -xzf kaiju.tar.gz
 ```
 
 :::note
-You must provide these databases pre-built to the pipeline, nf-core/taxprofiler neither comes with default databases not can generate databases for you.
+You must provide these databases pre-built to the pipeline, nf-core/taxprofiler neither comes with default databases nor can generate databases for you.
 For guidance on how to build databases, see the [Retrieving databases or building custom databases](#retrieving-databases-or-building-custom-databases) tutorial.
 :::
 

@@ -90,7 +90,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-save",
                     "description": "Save only the final reads from all read processing steps (that are sent to classification/profiling) in results directory.",
-                    "help_text": "This flag will generate the directory `results/analysis_read_reads` that contains the reads from the last preprocessing (QC, host removal, run merging etc.) step of the pipeline run. \n\nThis can be useful if you wish to re-use the final cleaned-up and prepared reads - the data actually used for the actual classification/profiling steps of the pipeline - for other analyses or purposes (e.g., to reduce redundant preprocessing between different pipelines, e.g. [nf-core/mag](https://nf-co.re/mag)).\n\nIn most cases this will be preferred over similar parameters e.g. ` --save_preprocessed_reads` or ` --save_complexityfiltered_reads`, unless you wish to explore in more detail the output of each specific preprocessing step independently.\n\nNote if you do no preprocessing of any kind, nothing will be present in this directory. "
+                    "help_text": "This flag will generate the directory `results/analysis_ready_reads` that contains the reads from the last preprocessing (QC, host removal, run merging etc.) step of the pipeline run. \n\nThis can be useful if you wish to re-use the final cleaned-up and prepared reads - the data actually used for the actual classification/profiling steps of the pipeline - for other analyses or purposes (e.g., to reduce redundant preprocessing between different pipelines, e.g. [nf-core/mag](https://nf-co.re/mag)).\n\nIn most cases this will be preferred over similar parameters e.g. ` --save_preprocessed_reads` or ` --save_complexityfiltered_reads`, unless you wish to explore in more detail the output of each specific preprocessing step independently.\n\nNote if you do no preprocessing of any kind, nothing will be present in this directory. "
                 }
             },
             "fa_icon": "fas fa-users-cog"
-Original file line number
+Diff line change
@@ Expand Up / @@ -59,7 +59,7 @@ tar -xzf kaiju.tar.gz @@
     ```
     :::note
-    You must provide these databases pre-built to the pipeline, nf-core/taxprofiler neither comes with default databases not can generate databases for you.
+    You must provide these databases pre-built to the pipeline, nf-core/taxprofiler neither comes with default databases nor can generate databases for you.
     For guidance on how to build databases, see the [Retrieving databases or building custom databases](#retrieving-databases-or-building-custom-databases) tutorial.
     :::
@@ Expand Down @@