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qdnaseq

A Nextflow pipeline to create qDNAseq bin annotations

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

Science Score: 31.0%

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    Found CITATION.cff file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Low similarity (14.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A Nextflow pipeline to create qDNAseq bin annotations

Basic Info
  • Host: GitHub
  • Owner: nf-cmgg
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 2.09 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Nextflow run with conda run with docker run with singularity Launch on Nextflow Tower

Introduction

CenterForMedicalGeneticsGhent/nf-cmgg-qdnaseq is a bioinformatics pipeline for creating qDNAseq annotations

  1. Create a mappability WIG file with GenMap
  2. Convert the WIG to BigWig with UCSC WigToBigWig
  3. Create the annotations using a custom R script

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,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.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 CenterForMedicalGeneticsGhent/nf-cmgg-qdnaseq \ -profile <docker/singularity/.../institute> \ --genome <genome> \ --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

CenterForMedicalGeneticsGhent/nf-cmgg-qdnaseq was originally written by nvnieuwk.

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: 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) 

# CenterForMedicalGeneticsGhent/nf-cmgg-qdnaseq: 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.

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.github/workflows/branch.yml actions
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.github/workflows/fix-linting.yml actions
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.github/workflows/linting.yml actions
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.github/workflows/linting_comment.yml actions
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modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/gawk/meta.yml cpan
modules/nf-core/genmap/index/meta.yml cpan
modules/nf-core/genmap/map/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/convert/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/merge/meta.yml cpan
modules/nf-core/tabix/bgzip/meta.yml cpan
modules/nf-core/ucsc/wigtobigwig/meta.yml cpan
modules/local/create_annotations/Dockerfile docker
  • mambaorg/micromamba 1.4-focal build
pyproject.toml pypi