From 1ef28d1c7ff41fad77479e2f05555ece85cc8c74 Mon Sep 17 00:00:00 2001
From: Lara Ianov <lianov@uab.edu>
Date: Thu, 3 Oct 2024 13:08:52 -0500
Subject: [PATCH] added additional custom.config tip

---
 README.md      | 16 +++++++++++++++-
 docs/output.md | 12 ++++++------
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 03284e1..d2132b5 100644
--- a/README.md
+++ b/README.md
@@ -163,6 +163,20 @@ process
 }
 ```
 
+We further note that while we encourage the use of `split_amount` as discussed above for larger datasets, the pipeline can be executed without enabling this parameter. When doing this, please consider increasing the time limit to `CORRECT_BARCODES` as it can take hours instead of minutes when `split_amount` is disabled:
+
+
+```groovy title="custom.config"
+//NOTE: with split_amount disabled, consider increasing the time limit to CORRECT_BARCODES
+process
+{
+    withName: '.*:CORRECT_BARCODES'
+    {
+        time = '15.h'
+    }
+}
+```
+
 ## Credits
 
 nf-core/scnanoseq was originally written by [Austyn Trull](https://github.com/atrull314), and [Dr. Lara Ianov](https://github.com/lianov).
@@ -170,7 +184,7 @@ nf-core/scnanoseq was originally written by [Austyn Trull](https://github.com/at
 We would also like to thank the following people and groups for their support, including financial support:
 
 - Dr. Elizabeth Worthey
-- University of Alabama at Birmingham Biological Data Science Core (U-BDS), RRID:SCR_021766, https://github.com/U-BDS
+- University of Alabama at Birmingham Biological Data Science Core (U-BDS), RRID:SCR_021766, <https://github.com/U-BDS>
 - Support from: 3P30CA013148-48S8
 
 ## Contributions and Support
diff --git a/docs/output.md b/docs/output.md
index f174bd2..9ddbf0a 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -28,8 +28,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [UCSC](#ucsc) - Annotation BED file
 - [Quality Control](#quality-control)
   - [FastQC](#fastqc) - FASTQ QC
-  - [Nanocomp](#nanocomp) - Long Read FASTQ QC
-  - [Nanoplot](#nanoplot) - Long Read FASTQ QC
+  - [NanoComp](#nanocomp) - Long Read FASTQ QC
+  - [NanoPlot](#nanoplot) - Long Read FASTQ QC
   - [ToulligQC](#toulligqc) - Long Read FASTQ QC
   - [RSeQC](#rseqc) - Various RNA-seq QC metrics
   - [Read Counts](#read-counts) - Read Counts QC
@@ -262,7 +262,7 @@ _High level statistics are provided in the MultiQC report, as show in this image
 The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
 :::
 
-### Nanocomp
+### NanoComp
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -280,9 +280,9 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 ![Nanocomp](images/nanocomp_1.png)
 ![Nanocomp](images/nanocomp_2.png)
 
-[Nanocomp](https://github.com/wdecoster/nanocomp) compares multiple runs of long read sequencing data and alignments. It creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot
+[NanoComp](https://github.com/wdecoster/nanocomp) compares multiple runs of long read sequencing data and alignments. It creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot
 
-### Nanoplot
+### NanoPlot
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -302,7 +302,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 ![Nanoplot](images/nanoplot_1.png)
 ![Nanoplot](images/nanoplot_2.png)
 
-[Nanoplot](https://github.com/wdecoster/NanoPlot) is a plotting tool for long read sequencing data and alignments.
+[NanoPlot](https://github.com/wdecoster/NanoPlot) is a plotting tool for long read sequencing data and alignments.
 
 ### ToulligQC