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rediscoverte

Pipeline for quantifying genome-wide TE expression in RNA sequencing data

https://github.com/mskcc/rediscoverte

Science Score: 44.0%

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    Found 9 DOI reference(s) in README
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Last synced: 6 months ago · JSON representation ·

Repository

Pipeline for quantifying genome-wide TE expression in RNA sequencing data

Basic Info
  • Host: GitHub
  • Owner: mskcc
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 188 KB
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

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

Introduction

msk/rediscoverte is a bioinformatics pipeline that quantifies genome-wide TE expression in RNA sequencing data. This is the nextflow pipeline for REdiscoverTE found here: https://github.com/ucsffrancislab/REdiscoverTE

  1. Index transcriptome (Salmon Index)
  2. Quantify reads (Salmon Quant)
  3. Run REdiscoverTE (REdiscoverTE)

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.

Running nextflow @ MSKCC

If you are runnning this pipeline on a MSKCC cluster you need to make sure nextflow is properly configured for the HPC envirornment:

bash module load java/jdk-17.0.8 module load singularity/3.7.1 export PATH=$PATH:/path/to/nextflow/binary export SINGULARITY_TMPDIR=/path/to/network/storage/for/singularity/tmp/files export NXF_SINGULARITY_CACHEDIR=/path/to/network/storage/for/singularity/cache

Running the pipeline

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq SAMPLE_SINGLE_END,input_R1.fq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

bash nextflow run main.nf \ -profile singularity,juno \ --input samplesheet.csv \ --outdir <OUTDIR>

[!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.

Credits

msk/rediscoverte was originally written by nikhil.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

Kong, Y., Rose, C.M., Cass, A.A. et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 10, 5228 (2019). https://doi.org/10.1038/s41467-019-13035-2

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: Memorial Sloan Kettering
  • Login: mskcc
  • Kind: organization
  • Email: perinj@mskcc.org
  • Location: New York, NY, USA

Citation (CITATIONS.md) 

# msk/rediscoverte: 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].

- [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.

## 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
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 23
  • Total Committers: 1
  • Avg Commits per committer: 23.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 23
  • Committers: 1
  • Avg Commits per committer: 23.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nikhil Kumar n****6@g****m 23

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 7 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 7 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
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  • nikhil (8)
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Dependencies

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modules/msk/rediscoverte/meta.yml cpan
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