Data

Tools

Indexes

Applications

Experiments

Open Source Science

odin

Module for variant calling and maf processing

https://github.com/mskcc/odin

Science Score: 44.0%

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
  • ✓
    DOI references
    Found 7 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Module for variant calling and maf processing

Basic Info
  • Host: GitHub
  • Owner: mskcc
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 5.01 MB
Statistics
  • Stars: 0
  • Watchers: 10
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Introduction

mskcc/odin is a bioinformatics pipeline that performs variant analysis on a pair of bams. The output is an annotated maf that is properly filtered and annotated.

ODIN diagram

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 pairId,tumorBam,normalBam,assay,normalType,bedFile pair_id,tumor.bam,normal.bam,assay,normalType,optional:regions.bed

Each row represents a pair of bam files and bait set.

For optional bed file, you can either enter a bed file leave it bank and one will be generated using covered intervals. To leave the field blank you can use any of these options:

csv pair_id,tumor.bam,normal.bam,assay,normalType,NONE pair_id,tumor.bam,normal.bam,assay,normalType,null pair_id,tumor.bam,normal.bam,assay,normalType,

Now, you can run the pipeline using:

nextflow run

bash nextflow run main.nf \ -profile singularity,test_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

mskcc/odin was originally written by C. Allan Bolipata.

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

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) 

# mskcc/odin: 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]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

- [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
  • Issues event: 1
  • Delete event: 1
Last Year
  • Issues event: 1
  • Delete event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 124
  • Total Committers: 6
  • Avg Commits per committer: 20.667
  • Development Distribution Score (DDS): 0.371
Past Year
  • Commits: 17
  • Committers: 5
  • Avg Commits per committer: 3.4
  • Development Distribution Score (DDS): 0.294
Top Committers
Name Email Commits
nikhil n****6@g****m 78
Allan Bolipata a****a@g****m 40
voyager pipeline user v****r@v****e 3
Tim s****t@m****g 1
Suleyman Vural s****l@g****m 1
Nicholas D. Socci s****n@m****g 1
Committer Domains (Top 20 + Academic)
mskcc.org: 2 voyager.cbio.private: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 2
  • Total pull requests: 23
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 12 days
  • Total issue authors: 1
  • Total pull request authors: 5
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.26
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 12
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.33
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • soccin (2)
Pull Request Authors
  • nikhil (15)
  • allanbolipata (6)
  • svural (2)
  • timosong (1)
  • soccin (1)
Top Labels
Issue Labels
bug (2)
Pull Request Labels
do not merge (1)

Dependencies

modules/local/vardictjava/meta.yml cpan
modules/nf-core/bcftools/annotate/meta.yml cpan
modules/nf-core/bcftools/concat/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
pyproject.toml pypi