address suggestions from Maxime

CHANGELOG.md

@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `demux_fast5` module to output demultiplexed fast5 files when `--output_demultiplex_fast5` is set
 - Add `--trim_barcodes` in Guppy basecaller to trim the barcodes from output fastq
 - Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
-  - Removed `--publish_dir_mode` as it is no longer required for the new syntax
+- Removed `--publish_dir_mode` as it is no longer required for the new syntax
 - Bump minimum Nextflow version from 21.04.0 -> 21.10.3
 - Update pipeline template to nf-core/tools `2.2`
 - Update `bambu` version from `1.0.2` to `2.0.0`

CITATIONS.md

@@ -12,20 +12,16 @@
 
 - [BEDTools](https://www.ncbi.nlm.nih.gov/pubmed/20110278/)
 
-* [cuteSV](https://pubmed.ncbi.nlm.nih.gov/32746918/)
+  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
+
+- [cuteSV](https://pubmed.ncbi.nlm.nih.gov/32746918/)
 
   > Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z, Liu Y, Liu B, Wang Y. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 2020 Aug 3;21(1):189. doi: 10.1186/s13059-020-02107-y. PMID: 32746918; PMCID: PMC7477834.
 
-* [DeepVariant](https://pubmed.ncbi.nlm.nih.gov/30247488/)
+- [DeepVariant](https://pubmed.ncbi.nlm.nih.gov/30247488/)
 
   > Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24. PMID: 30247488.
 
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-
-  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
-
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-
 - [featureCounts](https://www.ncbi.nlm.nih.gov/pubmed/24227677/)
 
   > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
@@ -44,14 +40,10 @@
 
   > Hendra C, et al., Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. bioRXiv (2021)
 
-* [PEPPER-Margin-DeepVariant](https://pubmed.ncbi.nlm.nih.gov/34725481/)
+- [PEPPER-Margin-DeepVariant](https://pubmed.ncbi.nlm.nih.gov/34725481/)
 
   > Shafin K, Pesout T, Chang PC, Nattestad M, Kolesnikov A, Goel S, Baid G, Kolmogorov M, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat Methods. 2021 Nov;18(11):1322-1332. doi: 10.1038/s41592-021-01299-w. Epub 2021 Nov 1. PMID: 34725481; PMCID: PMC8571015.
 
-* [pycoQC](https://doi.org/10.21105/joss.01236)
-
-  > Leger A, Leonardi T, (2019). pycoQC, interactive quality control for Oxford Nanopore Sequencing. Journal of Open Source Software, 4(34), 1236.
-
 - [Minimap2](https://pubmed.ncbi.nlm.nih.gov/29750242/)
 
   > Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

README.md

@@ -98,7 +98,7 @@ An example input samplesheet for performing both basecalling and demultiplexing
 
 nf-core/nanoseq was originally written by [Chelsea Sawyer](https://github.com/csawye01) and [Harshil Patel](https://github.com/drpatelh) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London. Other primary contributors include [Laura Wratten](https://github.com/lwratten), [Ying Chen](https://github.com/cying111), [Yuk Kei Wan](https://github.com/yuukiiwa) and [Jonathan Goeke](https://github.com/jonathangoeke) from the [Genome Institute of Singapore](https://www.a-star.edu.sg/gis), [Christopher Hakkaart](https://github.com/christopher-hakkaart) from [Institute of Medical Genetics and Applied Genomics](https://www.medizin.uni-tuebingen.de/de/das-klinikum/einrichtungen/institute/medizinische-genetik-und-angewandte-genomik), Germany, and [Johannes Alneberg](https://github.com/alneberg) and [Franziska Bonath](https://github.com/FranBonath) from [SciLifeLab](https://www.scilifelab.se/), Sweden.
 
-Many thanks to others who have helped out along the way too, including (but not limited to): [@crickbabs](https://github.com/crickbabs), [@AnnaSyme](https://github.com/AnnaSyme),[@ekushele](https://github.com/ekushele).
+Many thanks to others who have helped out along the way too, including (but not limited to): [@crickbabs](https://github.com/crickbabs), [@AnnaSyme](https://github.com/AnnaSyme), [@ekushele](https://github.com/ekushele).
 
 ## Contributions and Support
 

nextflow.config

@@ -195,13 +195,6 @@ if (!params.igenomes_ignore) {
     params.genomes = [:]
 }
 
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -241,7 +234,7 @@ manifest {
     description     = 'A pipeline to demultiplex, QC and map Nanopore data'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '2.0.1'
+    version         = '3.0.0'
 }
 
 // Load modules.config for DSL2 module specific options