Data

Tools

Indexes

Applications

Experiments

Open Source Science

dxnextflowrna

https://github.com/umcugenetics/dxnextflowrna

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: UMCUGenetics
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 698 KB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 0
  • Open Issues: 1
  • Releases: 4
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

umcugenetics/dxnextflowrna

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

umcugenetics/dxnextflowrna is a bioinformatics pipeline that can be used to analyse human RNA sequencing data. It takes FASTQ files as input, performs quality control (QC), trimming, filtering and alignment, and produces an extensive QC report.

umcugenetics/dxnextflowrna metro map

  1. Read QC (FastQC)
  2. Present QC for raw reads (MultiQC)
  3. Adapter and quality trimming (Trim Galore!)
  4. Removal of ribosomal RNA (SortMeRNA)
  5. Alignment (STAR)
  6. Merge, sort and index alignments (SAMtools)
  7. UMI-based deduplication (UMI-tools)
  8. Convert to CRAM (SAMtools)
  9. Extensive quality control:
    1. RSeQC
    2. Preseq
  10. Present QC (MultiQC)

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

  1. Create an input directory with sample's fastq files (paired, multiple lanes allowed.)
  2. Clone the github repository and all dependencies if required.
  3. Install bash sh install.sh
  4. Now, you can run the pipeline using:

bash <path_to_git_clone>/tools/nextflow/nextflow run \ <path_to_git_clone>/main.nf \ -c <path_to_git_clone>/nextflow.config \ --input <input> \ --outdir <output> \ --analysis_id <analysis_id> \ --email <email> \ -resume \ -ansi-log false \ -profile singularity \

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Developers: Instructions and reminders when changing DxNextflowRNA

[!WARNING] Please, try to keep using nfcore tools and guidelines!

Update files

When updating Nextflow

  • Update version by using nf-core pipelines bump-version --nextflow <new_nextflow_version>
  • Update version in install.sh and bash sh install.sh

Credits

umcugenetics/dxnextflowrna was originally written by UMCU Genetics.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

  • Name: UMCU Genetics
  • Login: UMCUGenetics
  • Kind: organization
  • Email: inijman@umcutrecht.nl
  • Location: Utrecht

Repository for genetics code

Citation (CITATIONS.md) 

# UMCUGenetics/DxNextflowRNA: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/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.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/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://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.

- [picard-tools](http://broadinstitute.github.io/picard)

- [preseq](https://pubmed.ncbi.nlm.nih.gov/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.

- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)

  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.

- [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.

- [SortMeRNA](https://pubmed.ncbi.nlm.nih.gov/23071270/)

  > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PubMed PMID: 23071270.

- [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.

- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)

  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.


## Software packaging/containerisation tools
- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/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.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/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.

GitHub Events

Total
  • Release event: 2
  • Delete event: 23
  • Issue comment event: 2
  • Push event: 159
  • Pull request review event: 51
  • Pull request review comment event: 45
  • Pull request event: 47
  • Create event: 16
Last Year
  • Release event: 2
  • Delete event: 23
  • Issue comment event: 2
  • Push event: 159
  • Pull request review event: 51
  • Pull request review comment event: 45
  • Pull request event: 47
  • Create event: 16

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 28
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 months
  • Total issue authors: 0
  • Total pull request authors: 5
  • Average comments per issue: 0
  • Average comments per pull request: 0.11
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 21
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.1
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • Jorisvansteenbrugge (16)
  • ellendejong (9)
  • rernst (1)
  • lonnekevanbrussel (1)
  • JadevDinter (1)
Top Labels
Issue Labels
Pull Request Labels
do not merge (1)