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nf-core_nano-fanconi

https://github.com/jiangyanyu/nf-core_nano-fanconi

Science Score: 44.0%

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    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: JiangyanYu
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 4.22 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 15
  • Releases: 0
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nano-fanconi is an nf-core based workflow to analyze nanopore long-read sequencing data for routine fanconi diagnosis. Description Basic steps to use the workflow: 1. Install nextflow according to its manual (https://www.nextflow.io/docs/latest/install.html) 2. Download and unzip (or git clone) nano-fanconi package from github (https://github.com/JiangyanYu/nf-corenano-fanconi.git) ``` git clone -b main https://github.com/JiangyanYu/nf-corenano-fanconi 4. Adjusting file path accordingly: 1) Sequencing data path in **/nf-core_nano-fanconi/assets/samplesheet.csv**. The file directory is the absolute path in your file system. <not needed: id is used to merge samples from different flow cells. Therefore, sample shall be different from id, otherwise merge_bam_sample will throw errors.> 2) Reference genome path in **/nf-core_nano-fanconi/profile.config**. Besides the reference path, annotsvAnnotations database directory as well as the dorado model details can be specified in this file. 3) Select packages to be used in **/nf-core_nano-fanconi/nextflow.config**. Annotate (true or false) the programs one likes to use. In the default setting, annotation part is marked as false. If needed, installation of annotation database is needed (see below). 4) Resource specification in **/nf-core_nano-fanconi/conf/base.config**. 5. Run the analysis by following command: nextflow run ./nf-corenano-fanconi/ \ # The path to the nano-fanconi package -profile nanofanconi,docker \ # Corresponding to the setting in /nf-corenano-fanconi/profile.config. Beaware that no space between nanofanconi,docker --outdir ./output # Specify the directory for output results. ```

Notes 1) the current annotsv docker image does not contain annotationsDir, thus need to be installed first (https://github.com/lgmgeo/AnnotSV/blob/master/bin/INSTALLannotations.sh). Then manually change the directory in the profile.config file. 2) Deepvariant modeltype is set as WGS

Cite us (to-be-updated): Nano-Fanconi: A Nextflow framework for automated analysis of Nanopore based long-read sequencing data for Fanconi anemia diagnosis.

Basic structure is from following repos (2024-12-10): \ 1. https://github.com/nf-core/nanoseq \ 2. https://github.com/dhslab/nf-core-wgsnano \ 2.1 since the firewall is restricted to docker, I have simply copied the dorado image from dhslab (https://github.com/dhslab/dhslab-docker-images/pkgs/container/docker-dorado) to my docker hub, version 241016. \ 2.2 same for https://github.com/dhslab/dhslab-docker-images/pkgs/container/docker-whatshap, version 240302.

Owner

  • Name: Jiangyan Yu
  • Login: JiangyanYu
  • Kind: user
  • Location: Bonn, Germany
  • Company: University of Bonn

Postdoc in the Schlitzer lab, LIMES, Bonn, Germany

Citation (CITATIONS.md) 

# jiangyanyu/nf-core_nano-fanconi: Citations
The formate is based on https://github.com/dhslab/nf-core-wgsnano

## [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/)

- [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)

- [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.

- [Sniffles](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990442/)

  > Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 Jun;15(6):461-468. doi: 10 1038/s41592-018-0001-7. Epub 2018 Apr 30. PMID: 29713083; PMCID: PMC5990442.

- [AnnotSV](https://academic.oup.com/bioinformatics/article/34/20/3572/4970516)
  > Geoffroy V, Herenger Y, Kress A, Stoetzel C, Piton A, Dollfus H, Muller J. AnnotSV: An integrated tool for Structural Variations annotation. Bioinformatics. 2018 Apr 14. doi: 10.1093/bioinformatics/bty304

- [Whatshap](https://doi.org/10.1093/bioinformatics/btw276)

  > Garg S, Martin M, Marschall T. Read-based phasing of related individuals. Bioinformatics 2016; 32 (12): i234-i242. doi: 10.1093/bioinformatics/btw276. PubMed PMID: 27307622; Pubmed Central PMCID: PMC4908360.

- [DeepVariant](https://pubmed.ncbi.nlm.nih.gov/30247488/)

  > Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24. PMID: 30247488.

GitHub Events

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Last Year
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Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 15
  • Total pull requests: 2
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 15
  • Pull requests: 2
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 1 hour
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • ChrisRem85 (11)
  • JiangyanYu (4)
Pull Request Authors
  • JiangyanYu (1)
Top Labels
Issue Labels
enhancement (11) bug (3) documentation (1)
Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 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/custom/dumpsoftwareversions/meta.yml cpan
docker_files/dorado/Dockerfile docker
  • nanoporetech/dorado sha8bc19cc3c78c1ce847fbf4a879cad997b7e8c430 build
pyproject.toml pypi