Merge pull request #88 from genomic-medicine-sweden/more_citations

adding more citations
genomic-medicine-sweden · Mar 13, 2024 · 5d24394 · 5d24394
2 parents 33cc55f + c57d8b2
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diff --git a/CHANGELOG.md b/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`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -14,7 +14,7 @@
 
   > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
 
-- [UCSC tools] (https://academic.oup.com/bioinformatics/article/26/17/2204/199001)
+- [UCSC tools](https://academic.oup.com/bioinformatics/article/26/17/2204/199001)
 
   > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351
 
@@ -26,10 +26,22 @@
 
   > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4
 
+- [DROP](https://www.nature.com/articles/s41596-020-00462-5)
+
+  > Yépez, V.A., Mertes, C., Müller, M.F. et al. Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 16, 1276–1296 (2021). doi:10.1038/s41596-020-00462-5
+
+- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)
+
+  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [FRASER](https://www.nature.com/articles/s41467-020-20573-7)
+
+  > Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER [published correction appears in Nat Commun. 2022 Jun 16;13(1):3474]. Nat Commun. 2021;12(1):529. Published 2021 Jan 22. doi:10.1038/s41467-020-20573-7
+
 - [GATK](https://genome.cshlp.org/content/20/9/1297)
 
   > McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-1303. doi:10.1101/gr.107524.110
@@ -42,6 +54,12 @@
 
   > 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.
 
+- [OUTRIDER](https://www.sciencedirect.com/science/article/pii/S0002929718304014?via%3Dihub)
+
+  > Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. Am J Hum Genet. 2018;103(6):907-917. doi:10.1016/j.ajhg.2018.10.025
+
+- [picard-tools](http://broadinstitute.github.io/picard)
+
 - [StringTie](http://ccb.jhu.edu/software/stringtie/)
 
   > Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PMID: 25690850; PMCID: PMC4643835.
@@ -50,6 +68,10 @@
 
   > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.
 
+- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)
+
+  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

diff --git a/nextflow.config b/nextflow.config
@@ -58,7 +58,7 @@ params {
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
-    multiqc_logo               = null
+    multiqc_logo               = "${projectDir}/assets/tomte_logo_light.png"
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
 

diff --git a/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf b/subworkflows/local/utils_nfcore_tomte_pipeline/main.nf
@@ -216,26 +216,48 @@ 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),",
+            "DROP (Yépez et al. 2021),",
+            params.switch_vep ? "EnsemblVEP (McLaren et al. 2016)," : "",
+            "fastp (Chen et al. 2018),",
             "FastQC (Andrews 2010),",
-            "MultiQC (Ewels et al. 2016)",
+            params.switch_drop_as ? "FRASER (Mertes et al 2021)," : "",
+            "GATK (McKenna et al. 2010),",
+            params.switch_stringtie ? "GFFCompare (Pertea et al. 2020), StringTie (Pertea et al. 2015)," : "",
+            "MultiQC (Ewels et al. 2016),",
+            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_build_tracks ? "UCSC tools (Kent et al. 2010)" : "",
             "."
         ].join(' ').trim()
 
     return citation_text
 }
 
 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>",
+            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>",
+            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>": ""
         ].join(' ').trim()
 
     return reference_text
@@ -252,12 +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_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text