adressing reviewer comments

genomic-medicine-sweden · Mar 13, 2024 · c57d8b2 · c57d8b2
1 parent 05bef35
commit c57d8b2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf b/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf
@@ -248,13 +248,13 @@ def toolBibliographyText() {
             "<li>Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 10 2012;29:15-21. doi:10.1093/bioinformatics/bts635</li>",
             "<li>Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England). 10 2016;32:3047-3048. doi:10.1093/BIOINFORMATICS/BTW354</li>",
             "<li>Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nature biotechnology. 3 2020;38:276-278. doi:10.1038/S41587-020-0439-X</li>",
-            "<li>Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 9 2010;26:2204-2207. doi:10.1093/BIOINFORMATICS/BTQ351</li>",
+            params.switch_build_tracks ? "<li>Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 9 2010;26:2204-2207. doi:10.1093/BIOINFORMATICS/BTQ351</li>" : "",
             "<li>Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PloS one. 5 2017;12. doi:10.1371/JOURNAL.PONE.0177459</li>",
             "<li>Leprevost FDV, Grüning BA, Aflitos SA, et al. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England). 8 2017;33:2580-2582. doi:10.1093/BIOINFORMATICS/BTX192</li>",
             "<li>McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 9 2010;20:1297-1303. doi:10.1101/GR.107524.110</li>",
             params.switch_vep ? "<li>McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome biology. 6 2016;17. doi:10.1186/S13059-016-0974-4</li>" : "",
             "<li>MerkelDirk. Docker. Linux Journal. Published online 3 2014. doi:10.5555/2600239.2600241</li>",
-            "<li>Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER. Nature Communications 2021 12:1. 1 2021;12:1-13. doi:10.1038/s41467-020-20573-7</li>",
+            params.switch_drop_as ? "<li>Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER. Nature Communications 2021 12:1. 1 2021;12:1-13. doi:10.1038/s41467-020-20573-7</li>" : "",
             "<li>Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods. 2017;14:417-419. doi:10.1038/NMETH.4197</li>",
             params.switch_stringtie ? "<li>Pertea M, Pertea G. GFF Utilities: GffRead and GffCompare. F1000Research. 9 2020;9:304. doi:10.12688/F1000RESEARCH.23297.1</li>" : "",
             params.switch_stringtie ? "<li>Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology. 2015;33:290-295. doi:10.1038/NBT.3122</li>": ""