From 105bac7bb9882561e2fc96db7b02a7ca3e06640b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 20 Apr 2023 12:59:33 +0200 Subject: [PATCH] Apply suggestions from code review --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index c562527..0fde197 100644 --- a/docs/output.md +++ b/docs/output.md @@ -259,7 +259,7 @@ This directory will be present and contain the unmapped reads from the `.fastq` -The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the \_last step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - those will be the ones present in this directory. +The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the _last_ step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - those will be the ones present in this directory. > ⚠️ If you turn off all preprocessing steps, then no results will be present in this directory. This happens independently for short- and long-reads. I.e. you will only have FASTQ files for short reads in this directory if you skip all long-read preprocessing.