Merge pull request #109 from drpatelh/master

Change all parameters to follow snake_case format

Author: drpatelh

CHANGELOG.md

@@ -13,7 +13,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Capitalised process names
 * Add quick start information to main README
 * Update template to tools `1.7`
-* Bump Nextflow version to `19.04.0`
+* Add `--trim_nextseq` parameter
+* Added `CITATIONS.md` file
 
 ### `Fixed`
 
@@ -23,9 +24,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
 * Increase default resource requirements in `base.config`
 * Increase process-specific requirements based on user-reported failures
+* Change parameter `saveGenomeIndex` to `save_reference`
+* Change parameter `--design` to `--input`
+* Change all parameters from `camelCase` to `snake_case`
+* Fixed bug in UpSetR peak intersection plot
 
 ### `Dependencies`
 
+* Bump Nextflow version to `19.04.0`
 
 ## [1.0.0] - 2019-06-06
 

CITATIONS.md

@@ -0,0 +1,101 @@
+# nf-core/chipseq: Citations
+
+## Pipeline tools
+
+* [Nextflow](https://www.ncbi.nlm.nih.gov/pubmed/28398311/)
+  > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+* [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.
+
+* [BEDTools](https://www.ncbi.nlm.nih.gov/pubmed/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.
+
+* [SAMtools](https://www.ncbi.nlm.nih.gov/pubmed/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.
+
+* [BamTools](https://www.ncbi.nlm.nih.gov/pubmed/21493652/)
+  > Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14. PubMed PMID: 21493652; PubMed Central PMCID: PMC3106182.
+
+* [UCSC tools](https://www.ncbi.nlm.nih.gov/pubmed/20639541/)
+  > 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. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.
+
+* [preseq](https://www.ncbi.nlm.nih.gov/pubmed/23435259/)
+  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.
+
+* [deepTools](https://www.ncbi.nlm.nih.gov/pubmed/27079975/)
+  > Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13. PubMed PMID: 27079975; PubMed Central PMCID: PMC4987876.
+
+* [MACS2](https://www.ncbi.nlm.nih.gov/pubmed/18798982/)
+  > Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715.
+
+* [HOMER](https://www.ncbi.nlm.nih.gov/pubmed/20513432/)
+  > Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89. doi: 10.1016/j.molcel.2010.05.004. PubMed PMID: 20513432; PubMed Central PMCID: PMC2898526.
+
+* [phantompeakqualtools](https://www.ncbi.nlm.nih.gov/pubmed/22955991/)
+  > Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111. PubMed PMID: 22955991; PubMed Central PMCID: PMC3431496.
+
+* [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.
+
+* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/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.
+
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+* [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+
+* [picard-tools](http://broadinstitute.github.io/picard)
+
+* [pysam](https://github.com/pysam-developers/pysam)
+
+## R packages
+
+* [R](https://www.R-project.org/)
+  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
+
+* [DESeq2](https://www.ncbi.nlm.nih.gov/pubmed/25516281/)
+  > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
+
+* [vsn](https://bioconductor.org/packages/release/bioc/html/vsn.html)
+  > Wolfgang Huber, Anja von Heydebreck, Holger Sueltmann, Annemarie Poustka and Martin Vingron. Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression. Bioinformatics 18, S96-S104 (2002).
+
+* [UpSetR](https://CRAN.R-project.org/package=UpSetR)
+  > Nils Gehlenborg (2017). UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets.
+
+* [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
+  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
+
+* [reshape2](http://www.jstatsoft.org/v21/i12/)
+  > Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20.
+
+* [scales](https://CRAN.R-project.org/package=scales)
+  > Hadley Wickham (2018). scales: Scale Functions for Visualization.
+
+* [pheatmap](https://CRAN.R-project.org/package=pheatmap)
+  > Raivo Kolde (2018). pheatmap: Pretty Heatmaps.
+
+* [lattice](https://cran.r-project.org/web/packages/lattice/index.html)
+  > Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5.
+
+* [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
+  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
+
+* [optparse](https://CRAN.R-project.org/package=optparse)
+  > Trevor L Davis (2018). optparse: Command Line Option Parser.
+
+* [xfun](https://CRAN.R-project.org/package=xfun)
+  > Yihui Xie (2018). xfun: Miscellaneous Functions by 'Yihui Xie'.
+
+## Software packaging/containerisation tools
+
+* [Bioconda](https://www.ncbi.nlm.nih.gov/pubmed/29967506/)
+  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+* [Anaconda](https://anaconda.com)
+  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+* [Singularity](https://www.ncbi.nlm.nih.gov/pubmed/28494014/)
+  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+
+* [Docker](https://www.docker.com/)

Dockerfile

@@ -4,4 +4,5 @@ LABEL authors="Philip Ewels" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
+RUN conda env export --name nf-core-chipseq-1.0.1dev > nf-core-chipseq-1.0.1dev.yml
 ENV PATH /opt/conda/envs/nf-core-chipseq-1.0.1dev/bin:$PATH

README.md

@@ -60,7 +60,7 @@ nextflow run nf-core/chipseq -profile test,<docker/singularity/conda>
 iv. Start running your own analysis!
 
 ```bash
-nextflow run nf-core/chipseq -profile <docker/singularity/conda> --design design.csv --genome GRCh37
+nextflow run nf-core/chipseq -profile <docker/singularity/conda> --input design.csv --genome GRCh37
 ```
 
 See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
@@ -96,3 +96,6 @@ If you use nf-core/chipseq for your analysis, please cite it using the following
 
 You can cite the `nf-core` pre-print as follows:  
 > Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
+
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+

bin/check_design.py

@@ -2,7 +2,7 @@
 
 #######################################################################
 #######################################################################
-## Created on April 4th 2019 to reformat nf-core/chipseq design file
+## Created on April 4th 2019 to check nf-core/chipseq design file
 #######################################################################
 #######################################################################
 
@@ -18,7 +18,7 @@
 ############################################
 
 Description = 'Reformat nf-core/chipseq design file and check its contents.'
-Epilog = """Example usage: python reformat_design.py <DESIGN_FILE_IN> <DESIGN_FILE_OUT>"""
+Epilog = """Example usage: python check_design.py <DESIGN_FILE_IN> <DESIGN_FILE_OUT>"""
 
 argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
 

bin/plot_peak_intersect.r

@@ -45,14 +45,28 @@ comb.dat <- read.table(opt$input_file,sep="\t",header=FALSE)
 comb.vec <- comb.dat[,2]
 comb.vec <- setNames(comb.vec,comb.dat[,1])
 
-pdf(opt$output_file,onefile=F,height=10,width=14)
-
-upset(fromExpression(comb.vec),
-      sets.bar.color = "#56B4E9",
-      point.size = 5,
-      line.size = 2,
-      order.by = "freq",
-      text.scale = c(1.7, 1.5, 1.7, 1.5, 1.7, 1.7))
+sets <- sort(unique(unlist(strsplit(names(comb.vec),split='&'))), decreasing = TRUE)
+nintersects = length(names(comb.vec))
+if (nintersects > 70) {
+    nintersects <- 70
+}
+
+pdf(opt$output_file,onefile=F,height=10,width=20)
+
+upset(
+    fromExpression(comb.vec),
+    nsets = length(sets),
+    nintersects = nintersects,
+    sets = sets,
+    keep.order = TRUE,
+    sets.bar.color = "#56B4E9",
+    point.size = 3,
+    line.size = 1,
+    mb.ratio = c(0.55, 0.45),
+    order.by = "freq",
+    number.angles = 30,
+    text.scale = c(1.5, 1.5, 1.5, 1.5, 1.5, 1.2)
+)
 
 dev.off()
 

conf/test.config

@@ -16,7 +16,7 @@ params {
   max_time = 12.h
 
   // Input data
-  design = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv'
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv'
 
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa'