adding citations, remove typos

Author: CaroAMN

CITATIONS.md

@@ -10,23 +10,31 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [NuMorph](https://pubmed.ncbi.nlm.nih.gov/34644582/)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL. NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images. Cell Rep. 2021 Oct 12;37(2):109802. doi: 10.1016/j.celrep.2021.109802. PMID: 34644582; PMCID: PMC8530274.
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [BaSiC](https://www.nature.com/articles/ncomms14836)
 
-> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Peng, T., Thorn, K., Schroeder, T. et al. A BaSiC tool for background and shading correction of optical microscopy images. Nat Commun 8, 14836 (2017). https://doi.org/10.1038/ncomms14836
 
-## Software packaging/containerisation tools
+- [elastix](https://pubmed.ncbi.nlm.nih.gov/19923044/)
+
+> Klein S, Staring M, Murphy K, Viergever MA, Pluim JP. elastix: a toolbox for intensity-based medical image registration. IEEE Trans Med Imaging. 2010 Jan;29(1):196-205. doi: 10.1109/TMI.2009.2035616. Epub 2009 Nov 17. PMID: 19923044.
+
+- [3DUnetCNN](https://pubmed.ncbi.nlm.nih.gov/37555134/)
 
-- [Anaconda](https://anaconda.com)
+> Ellis DG, Aizenberg MR. Structural Brain Imaging Predicts Individual-Level Task Activation Maps Using Deep Learning. Front Neuroimaging. 2022 Apr 18;1:834883. doi: 10.3389/fnimg.2022.834883. PMID: 37555134; PMCID: PMC10406267.
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+[VLFeat](https://www.vlfeat.org/)
 
-- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+> A. Vedaldi and B. Fulkerson VLFeat: An Open and Portable Library of Computer Vision Algorithms (2008)
 
-  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+
+## Software packaging/containerisation tools
 
 - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 

README.md

@@ -21,13 +21,13 @@
 
 ## Introduction
 
-**nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleard samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignemnt, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a regsitration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.
+**nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleared samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignment, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a registration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.
 
 <div style="text-align: center;">
 <img src="docs/images/lsmquant-metromap.svg" alt="lasmquant metromap">
 </div>
 
-### Basic workflow
+## Basic workflow
 
 **Preprocessing**
 

conf/base.config

@@ -26,8 +26,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }

modules/local/mat2json/main.nf

@@ -11,7 +11,7 @@ process MAT2JSON {
 
     output:
     tuple val(meta), path("${process}/*/*.*"),     emit: converted_file
-    path "versions.yml"              ,     emit: versions
+    path "versions.yml"                      ,     emit: versions
 
     when:
     task.ext.when == null || task.ext.when