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forte

Functional Observation of RNA Transcriptome Elements/Expression

https://github.com/mskcc/forte

Science Score: 57.0%

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

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    DOI references
    Found 7 DOI reference(s) in README
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    Low similarity (15.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Functional Observation of RNA Transcriptome Elements/Expression

Basic Info
  • Host: GitHub
  • Owner: mskcc
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 22.3 MB
Statistics
  • Stars: 8
  • Watchers: 15
  • Forks: 2
  • Open Issues: 36
  • Releases: 1
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

FORTE

Introduction

mskcc/forte is a best-practice analysis pipeline for bulk RNAseq.

  • Functional
  • Observation of
  • RNA
  • Transcriptome
  • Elements/Expression

Features

  1. Read pre-processing
    1. Trimming
    2. UMI extraction and deduplication
  2. Alignment
  3. Transcript quantification
  4. Fusion calling and annotation
  5. FASTQ and BAM QC
  6. Fillouts

Quick Start

  1. Install Nextflow (>=21.10.3)

  2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

  3. Clone the pipeline repository and test it on a minimal dataset with the following steps:

bash nextflow run /path/to/clonedrepo/main.nf -profile test,singularity --outdir <OUTDIR>

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

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. :::

Now, you can run the pipeline using:

bash nextflow run /path/to/clonedrepo/main.nf \ --input samplesheet.csv \ --outdir <OUTDIR> \ --genome GRCh37 \ -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.

Credits

mskcc/forte was originally written by Anne Marie Noronha noronhaa@mskcc.org.

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

We also thank the following contributors:

Contributions and Support

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

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

Citation (CITATIONS.md) 

# mskcc/forte: 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

- [fastp](https://doi.org/10.1093/bioinformatics/bty560)

  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560

- [UMI-tools](https://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract)

  > 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. PMID: 28100584; PMCID: PMC5340976.

- [STAR](https://academic.oup.com/bioinformatics/article/29/1/15/272537?login=false)

  > 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. PMID: 23104886; PMCID: PMC3530905.

- [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
  • Create event: 22
  • Issues event: 24
  • Watch event: 3
  • Delete event: 17
  • Issue comment event: 30
  • Push event: 153
  • Pull request review comment event: 20
  • Pull request review event: 56
  • Gollum event: 1
  • Pull request event: 30
  • Fork event: 1
Last Year
  • Create event: 22
  • Issues event: 24
  • Watch event: 3
  • Delete event: 17
  • Issue comment event: 30
  • Push event: 153
  • Pull request review comment event: 20
  • Pull request review event: 56
  • Gollum event: 1
  • Pull request event: 30
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 346
  • Total Committers: 4
  • Avg Commits per committer: 86.5
  • Development Distribution Score (DDS): 0.147
Past Year
  • Commits: 24
  • Committers: 3
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.208
Top Committers
Name Email Commits
Anne Marie Noronha a****4 295
Alexandria Pinto p****1@m****g 30
Anne Marie Noronha n****a@m****g 19
EC2 Default User e****r@i****l 2
Committer Domains (Top 20 + Academic)
mskcc.org: 2 ip-10-6-50-7.ec2.internal: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 58
  • Total pull requests: 79
  • Average time to close issues: 2 months
  • Average time to close pull requests: 14 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.53
  • Average comments per pull request: 0.32
  • Merged pull requests: 64
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 15
  • Pull requests: 21
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 2 months
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.2
  • Average comments per pull request: 1.1
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • anoronh4 (55)
  • pintoa1-mskcc (3)
  • tpereachamblee (1)
Pull Request Authors
  • anoronh4 (73)
  • pintoa1-mskcc (10)
Top Labels
Issue Labels
enhancement (20) bug (12) backburner (6) question (2) documentation (2) nf-core update (1)
Pull Request Labels
bug (2)

Dependencies

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.github/workflows/branch.yml actions
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.github/workflows/ci.yml actions
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.github/workflows/linting_comment.yml actions
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.github/workflows/release-announcments.yml actions
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modules/local/agfusion/batch/meta.yml cpan
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modules/local/fusioncatcher/detect/meta.yml cpan
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modules/local/starfusion/detect/meta.yml cpan
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modules/local/ucsc/genepredtobed/meta.yml cpan
modules/msk/gbcms/meta.yml cpan
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modules/nf-core/rseqc/bamstat/meta.yml cpan
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modules/nf-core/samtools/bam2fq/meta.yml cpan
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modules/nf-core/samtools/index/meta.yml cpan
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modules/local/agfusion/container/Dockerfile docker
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modules/local/metafusion/container/Dockerfile docker
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modules/local/oncokb/fusionannotator/container/Dockerfile docker
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