Merge branch 'dev' into nf-core-template-merge-3.0.2

.gitpod.yml

@@ -7,8 +7,9 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    #{%- if code_linters -%}
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
     - nextflow.nextflow # Nextflow syntax highlighting

CHANGELOG.md

@@ -3,12 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v0.0.1dev - [date]
+## 0.0.1dev - [2024-10-16]
 
 Initial release of nf-core/circrna, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
+- Multiple methods for BSJ detection (CIRIquant, find_circ, segemehl, mapsplice, circexplorer2, circrna_finder, DCC)
+- Multiple methods for circRNA quantification (psirc-quant, CIRIquant, sum and max aggregations)
+- DB and GTF-based circRNA annotation
+- MiRNA target prediction (TargetScan, miRanda) and correlation analysis
+- Basic statistical analyses (CircTest, CIRIquant differential expression)
+
 ### `Fixed`
 
 ### `Dependencies`

CITATIONS.md

@@ -10,14 +10,158 @@
 
 ## Pipeline tools
 
+- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
+
+  > 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.
+
+- [Bowtie](https://doi.org/10.1186/gb-2009-10-3-r25)
+
+  > Langmead, B., Trapnell, C., Pop, M. et al., 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25. doi: 10.1186/gb-2009-10-3-r25
+
+- [Bowtie2](https:/dx.doi.org/10.1038/nmeth.1923)
+
+  > Langmead, B. and Salzberg, S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. doi: 10.1038/nmeth.1923.
+
+- [BWA](https://www.ncbi.nlm.nih.gov/pubmed/19451168/)
+
+  > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234.
+
+- [CIRCexplorer2](https://doi.org/10.1101/gr.202895.115)
+
+  > Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. (2016). Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87.
+
+- [circRNA finder](https://doi.org/10.1016/j.celrep.2014.10.062)
+
+  > Westholm, J.O., Lai, E.C., et al. (2016). Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation Westholm et al. Cell Reports.
+
+- [CIRIquant](https://doi.org/10.1038/s41467-019-13840-9)
+
+  > Zhang, J., Chen, S., Yang, J. et al. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11, 90.
+
+- [DCC](https://doi.org/10.1093/bioinformatics/btv656)
+
+  > Jun Cheng, Franziska Metge, Christoph Dieterich, (2016). Specific identification and quantification of circular RNAs from sequencing data, Bioinformatics, 32(7), 1094–1096.
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [find circ](https://doi.org/10.1038/nature11928)
+
+  > Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338.
+
+- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)
+
+  > 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 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.
+
+- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)
+
+  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.
+
+- [MapSplice2](https://doi.org/10.1093/nar/gkq622)
+
+  > Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178.
+
+- [miRanda](https://doi.org/10.1186/gb-2003-5-1-r1)
+
+  > Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.
+
+- [find circ](https://doi.org/10.1038/nature11928)
+
+  > Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338.
+
+- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)
+
+  > 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 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.
+
+- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)
+
+  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.
+
+- [MapSplice2](https://doi.org/10.1093/nar/gkq622)
+
+  > Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178.
+
+- [miRanda](https://doi.org/10.1186/gb-2003-5-1-r1)
+
+  > Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.
+
 - [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.
 
+- [R](https://www.R-project.org/)
+
+  > R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
+
+  - [biomaRt](https://doi.org/10.1038/nprot.2009.97)
+
+    > Durinck S, Spellman PT, Birney E, Huber W. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 4(8):1184-91.
+
+  - [circlize](https://doi.org/10.1093/bioinformatics/btu393)
+
+    > Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors (2014). circlize implements and enhances circular visualization in R , Bioinformatics, 30,(19) 2811–2812.
+
+  - [DESeq2](https://doi.org/10.1186/s13059-014-0550-8)
+
+    > Love, M.I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550.
+
+  - [EnhancedVolcano](https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html)
+
+    > Blighe K, Rana S, Lewis M (2020). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling.
+
+  - [ggplot2](https://ggplot2.tidyverse.org)
+
+    > Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4.
+
+  - [ggpubr](https://rpkgs.datanovia.com/ggpubr/)
+
+    > Kassambara A. (2020). ggpubr: 'ggplot2' Based Publication Ready Plots.
+
+  - [ihw](https://doi.org/10.1038/nmeth.3885)
+
+    > Ignatiadis, N., Klaus, B., Zaugg, J. et al. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods 13, 577–580.
+
+  - [PCAtools](https://bioconductor.org/packages/release/bioc/html/PCAtools.html)
+
+    > Blighe K, Lun A (2020). PCAtools: PCAtools: Everything Principal Components Analysis.
+
+  - [pheatmap](https://cran.r-project.org/package=pheatmap)
+
+    > Kolde, R. (2019) Pretty Heatmaps.
+
+  - [pvclust](https://doi.org/10.1093/bioinformatics/btl117)
+
+    > Suzuki R., Shimodaira H., (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22(12), 1540–1542.
+
+- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
+
+  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
+
+- [Segemehl](https://doi.org/10.1371/journal.pcbi.1000502)
+
+  > Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502.
+
+- [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.
+
+- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)
+
+  > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.
+
+- [TargetScan](https://doi.org/10.7554/elife.05005)
+
+  > Agarwal V, Bell GW, Nam JW, Bartel DP. (2015). Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4:e05005.
+
+- [ViennaRNA](https://doi.org/10.1186/1748-7188-6-26)
+
+  > Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26.
+
+## Test data References
+
+> Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021 Nov 5;219(3):iyab145. doi: 10.1093/genetics/iyab145. PMID: 34740247; PMCID: PMC8570788.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)