adressing comments and adding bibliography

CHANGELOG.md

@@ -16,6 +16,7 @@ Release of genomic-medicine-sweden/tomte, created with the [nf-core](https://nf-
 - A new parameter `vep_plugin_files` to supply files required by vep plugins [#67](https://github.com/genomic-medicine-sweden/tomte/pull/67)
 - The possibility of using `igenomes_base` to point to a path where genome specific reference files are placed (fasta, fai, gtf, star_index, salmon_index, subsample_bed) [#76](https://github.com/genomic-medicine-sweden/tomte/pull/76)
 - Merging of case's vcf files [#80](https://github.com/genomic-medicine-sweden/tomte/pull/80)
+- Reference list to MultiQC report [#88](https://github.com/genomic-medicine-sweden/tomte/pull/88)
 
 ### `Fixed`
 

subworkflows/local/utils_nfcore_tomte_pipeline/main.nf

@@ -216,9 +216,6 @@ def genomeExistsError() {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
             "BCFtools (Danecek et al. 2021),",
@@ -228,13 +225,12 @@ def toolCitationText() {
             "FastQC (Andrews 2010),",
             params.switch_drop_as ? "FRASER (Mertes et al 2021)," : "",
             "GATK (McKenna et al. 2010),",
-            params.switch_stringtie ? "GFFCompare (Pertea et al. 2020)," : "",
+            params.switch_stringtie ? "GFFCompare (Pertea et al. 2020), StringTie (Perteat et al. 2015)," : "",
             "MultiQC (Ewels et al. 2016),",
-            params.switch_drop_as ? "OUTRIDER (Brechtmann et al. 2018)," : "",
+            params.switch_drop_ae ? "OUTRIDER (Brechtmann et al. 2018)," : "",
             "SAMtools (Danecek et al. 2021),",
             "Salmon (Patro et al. 2017),",
             "STAR (Dobin et al. 2012),",
-            params.switch_stringtie ? "StringTie (Perteat et al. 2015)," : "",
             params.switch_build_tracks ? "UCSC tools (Kent et al. 2010)" : "",
             "."
         ].join(' ').trim()
@@ -243,12 +239,25 @@ def toolCitationText() {
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
             "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+            params.switch_drop_ae ? "<li>Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. The American Journal of Human Genetics. 12 2018;103:907-917. doi:10.1016/J.AJHG.2018.10.025</li>" : "",
+            "<li>Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England). 9 2018;34:i884-i890. doi:10.1093/BIOINFORMATICS/BTY560</li>",
+            "<li>Dale R, Grüning B, Sjödin A, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature methods. 7 2018;15:475-476. doi:10.1038/S41592-018-0046-7</li>",
+            "<li>Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 1 2021;10:1-4. doi:10.1093/GIGASCIENCE/GIAB008</li>",
+            "<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>",
+            "<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>",
+            "<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>": ""
         ].join(' ').trim()
 
     return reference_text
@@ -265,12 +274,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
-    //meta["tool_citations"] = ""
-    meta["tool_bibliography"] = ""
-
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
     meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    // meta["tool_bibliography"] = toolBibliographyText()
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text