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exomecnv

A nextflow pipeline for calling exome CNVs

https://github.com/nf-cmgg/exomecnv

Science Score: 57.0%

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    Found .zenodo.json file
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    DOI references
    Found 13 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

A nextflow pipeline for calling exome CNVs

Basic Info
  • Host: GitHub
  • Owner: nf-cmgg
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 2.75 MB
Statistics
  • Stars: 11
  • Watchers: 1
  • Forks: 3
  • Open Issues: 5
  • Releases: 7
Created over 2 years ago · Last pushed 10 months 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

nf-cmgg/exomecnv is a bioinformatics pipeline that can be used to call copy number variations (CNVs) from exome sequencing data with ExomeDepth and annotate these with EnsemblVEP. It takes a samplesheet with CRAM or BAM files and their index files as input, generates read count data, calls CNVs and ends with an annotation. It is also possible to take a samplesheet with VCF files and their index files as input and only execute the annotation.

Pipeline Summary

  1. Input samplesheet check
  2. Convert CRAM to BAM if CRAM files are provided (optional)
  3. ExomeDepth counting per sample (autosomal and chrX are separated)
  4. Merge count files per batch (autosomal and chrX remain separated)
  5. ExomeDepth CNV calling per sample (autosomal and chrX remain separated)
  6. Merge CNV calling files per sample (autosomal and chrX are merged)
  7. Convert merged files to VCF
  8. Generate index files for these VCF files
  9. Annotate VCF files with EnsemblVEP

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.

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

samplesheet.csv:

csv sample,batch,family,cram,crai,vcf,tbi sample1,prep_M,Fam1,/path/to/sample1.cram,/path/to/sample1.crai sample2,prep_F,Fam2,/path/to/sample2.cram,/path/to/sample2.crai,/path/to/sample2.vcf,/path/to/sample2.vcf.tbi

Each row represents a sample with the associated batch and family, followed by the optional paths to the CRAM/CRAI and/or VCF/TBI files, depending on which tasks should be executed.

Now, you can run the pipeline using:

bash nextflow run nf-cmgg/exomecnv \ -profile <docker/conda> \ --input /path/to/samplesheet.csv \ --outdir /path/to/outdir \ --vep_cache /path/to/vep_cache \ --exomedepth \ --annotate

to execute the ExomeDepth workflow, followed by an EnsemblVEP annotation on CRAM/CRAI (or BAM/BAI) files provided in the samplesheet. The --annotate parameter is optional. If not provided, only the ExomeDepth workflow will be executed. It is also possible to run the pipeline using:

bash nextflow run nf-cmgg/exomecnv \ -profile <docker/conda> \ --input /path/to/samplesheet.csv \ --outdir /path/to/outdir \ --vep_cache /path/to/vep_cache

to skip the ExomeDepth workflow and only execute the EnsemblVEP annotation on VCF/TBI files provided in the samplesheet.

[!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

nf-cmgg/exomecnv was originally written by BertGalle and Toros.

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

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: Center For Medical Genetics Ghent - Nextflow workflows
  • Login: nf-cmgg
  • Kind: organization
  • Email: ict@cmgg.be
  • Location: Belgium

Center For Medical Genetics Ghent - Ghent University Hospital - Nextflow workflows

Citation (CITATIONS.md) 

# nf-cmgg/exomecnv: 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

- [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. PMID: 19505943; PMCID: PMC2723002.

- [BedGoVcf](https://github.com/nvnieuwk/bedgovcf)

- [ExomeDepth](https://pubmed.ncbi.nlm.nih.gov/22942019/)

  > Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, Wood NW, Hambleton S, Burns SO, Thrasher AJ, Kumararatne D, Doffinger R, Nejentsev S. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012 Nov 1;28(21):2747-54. doi: 10.1093/bioinformatics/bts526. Epub 2012 Aug 31. PMID: 22942019; PMCID: PMC3476336.

- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/)

  > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825.

- [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: 13
  • Issues event: 7
  • Release event: 4
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 2
  • Push event: 63
  • Pull request review event: 37
  • Pull request review comment event: 22
  • Pull request event: 35
Last Year
  • Create event: 13
  • Issues event: 7
  • Release event: 4
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 2
  • Push event: 63
  • Pull request review event: 37
  • Pull request review comment event: 22
  • Pull request event: 35

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 10
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 18 hours
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.1
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 10
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 18 hours
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.1
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ToonRosseel (3)
  • matthdsm (1)
Pull Request Authors
  • ToonRosseel (19)
  • nvnieuwk (6)
  • BertGalle (5)
  • matthdsm (3)
  • ThomasSte01 (1)
Top Labels
Issue Labels
enhancement (4)
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Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v4 composite
  • actions/setup-node v4 composite
.github/workflows/linting.yml actions
  • actions/checkout v4 composite
  • actions/setup-node v4 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/multiqc/meta.yml cpan
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • nf-core/setup-nextflow v1 composite
modules/nf-core/samtools/convert/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
modules/nf-core/bedgovcf/meta.yml cpan
modules/nf-core/ensemblvep/vep/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
.github/workflows/template_version_comment.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
  • nichmor/minimal-read-yaml v0.0.2 composite
modules/nf-core/multiqc/environment.yml conda
  • multiqc 1.25.1.*
modules/nf-core/ensemblvep/download/meta.yml cpan
subworkflows/nf-core/utils_nfschema_plugin/meta.yml cpan
modules/local/custom/mergecnv/environment.yml pypi
modules/local/custom/mergecounts/environment.yml pypi
modules/local/exomedepth/call/environment.yml pypi
modules/local/exomedepth/count/environment.yml pypi
modules/nf-core/bedgovcf/environment.yml pypi
modules/nf-core/ensemblvep/download/environment.yml pypi
modules/nf-core/ensemblvep/vep/environment.yml pypi
modules/nf-core/samtools/convert/environment.yml pypi
modules/nf-core/tabix/tabix/environment.yml pypi