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bulk-foodie-pipeline

https://github.com/zhangzhen/bulk-foodie-pipeline

Science Score: 57.0%

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

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: zhangzhen
  • Language: Nextflow
  • Default Branch: main
  • Size: 255 KB
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 9 months ago · Last pushed 6 months ago
Metadata Files
Readme Citation

README.md

zhangzhen/bulkfoodiepipeline

Introduction

zhangzhen/bulkfoodiepipeline is a bioinformatics pipeline used for in-vivo bulk FOODIE sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads, computes conversion rates of cytosines, and calls footprints of transcription factors.

<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads (MultiQC)

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 zhangzhen/bulkfoodiepipeline \ -profile conda \ --input samplesheet.csv \ --depth <NUM> \ --expected_ratio_file <EXPECTED_RATIO_FILE> \ --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

zhangzhen/bulkfoodiepipeline was originally written by Zhang Zhen, Shen Ke, Wang Quangui.

We thank the following people for their extensive assistance in the development of this pipeline: - group members at Sunney Xie Lab

Contributions and Support

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

Citations

If you use bulk-foodie-pipeline for your analysis, please cite the FOODIE article as follows:

R. He, W. Dong, Z. Wang, C. Xie, L. Gao, W. Ma, K. Shen, D. Li, Y. Pang, F. Jian, J. Zhang, Y. Yuan, X. Wang, Z. Zhang, Y. Zheng, S. Liu, C. Luo, X. Chai, J. Ren, Z. Zhu, & X.S. Xie, Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase, Proc. Natl. Acad. Sci. U.S.A. 121 (52) e2423270121, doi: 10.1073/pnas.2423270121 (2024).

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: Zhang Zhen
  • Login: zhangzhen
  • Kind: user

I'm a PhD in Bioinformatics.

Citation (CITATIONS.md) 

# zhangzhen/bulkfoodiepipeline: 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

- [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

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Dependencies

modules/local/callratioanddepth/meta.yml cpan
modules/local/calltrack/meta.yml cpan
modules/local/highscorepeaks/meta.yml cpan
modules/local/igvtools/totdf/meta.yml cpan
modules/local/methylextract/meta.yml cpan
modules/local/plot/meta.yml cpan
modules/local/plottss/meta.yml cpan
modules/local/postprocessbed/meta.yml cpan
modules/nf-core/bedtools/bamtobed/meta.yml cpan
modules/nf-core/bedtools/genomecov/meta.yml cpan
modules/nf-core/bedtools/intersect/meta.yml cpan
modules/nf-core/bismark/align/meta.yml cpan
modules/nf-core/bismark/deduplicate/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/macs2/callpeak/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/trimgalore/meta.yml cpan
modules/nf-core/ucsc/bedgraphtobigwig/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
modules/local/callratioanddepth/environment.yml conda
  • numpy 1.23.5.*
  • pandas 2.0.3.*
  • python 3.10.*
  • scipy 1.10.1.*
modules/local/calltrack/environment.yml conda
  • python 3.10.*
modules/local/highscorepeaks/environment.yml conda
  • gawk 5.1.0.*
modules/local/igvtools/totdf/environment.yml conda
  • igvtools 2.17.3.*
modules/local/methylextract/environment.yml conda
  • numpy 1.23.5.*
  • pysam 0.19.1.*
  • python 3.10.*
modules/local/plot/environment.yml conda
  • r-base 4.2.1.*
  • r-ggplot2 3.4.4.*
  • r-reshape2 1.4.4.*
modules/local/plottss/environment.yml conda
  • r-base 4.3.3.*
  • r-data.table 1.17.0.*
  • r-dplyr 1.1.4.*
  • r-ggplot2 3.4.4.*
modules/local/postprocessbed/environment.yml conda
  • gawk 5.1.0.*
modules/nf-core/bedtools/bamtobed/environment.yml conda
  • bedtools 2.31.1.*
modules/nf-core/bedtools/genomecov/environment.yml conda
  • bedtools 2.31.1.*
modules/nf-core/bedtools/intersect/environment.yml conda
  • bedtools 2.31.1.*
modules/nf-core/bismark/align/environment.yml conda
  • bismark 0.24.2.*
modules/nf-core/bismark/deduplicate/environment.yml conda
  • bismark 0.24.2.*
modules/nf-core/fastqc/environment.yml conda
  • fastqc 0.12.1.*
modules/nf-core/macs2/callpeak/environment.yml conda
  • macs2 2.2.9.1.*
modules/nf-core/multiqc/environment.yml conda
  • multiqc 1.27.*
modules/nf-core/samtools/index/environment.yml conda
  • htslib 1.21.*
  • samtools 1.21.*
modules/nf-core/samtools/sort/environment.yml conda
  • htslib 1.21.*
  • samtools 1.21.*
modules/nf-core/trimgalore/environment.yml conda
  • cutadapt 4.9.*
  • pigz 2.8.*
  • trim-galore 0.6.10.*
modules/nf-core/ucsc/bedgraphtobigwig/environment.yml conda
  • ucsc-bedgraphtobigwig 469.*
modules/local/footprintext/meta.yml cpan
modules/local/getfpcounts/meta.yml cpan
modules/local/getopenregion/meta.yml cpan
modules/local/getuninfosites/meta.yml cpan
modules/local/gnu/cut/meta.yml cpan
modules/local/gnu/tail/meta.yml cpan
modules/nf-core/bedtools/merge/meta.yml cpan
modules/nf-core/gawk/meta.yml cpan
modules/nf-core/gnu/sort/meta.yml cpan
modules/nf-core/tabix/bgziptabix/meta.yml cpan
subworkflows/local/footprinting/meta.yml cpan
modules/local/footprintext/environment.yml pypi
modules/local/getfpcounts/environment.yml pypi
modules/local/getopenregion/environment.yml pypi
modules/local/getuninfosites/environment.yml pypi
modules/local/gnu/cut/environment.yml pypi
modules/local/gnu/tail/environment.yml pypi
modules/nf-core/bedtools/merge/environment.yml pypi
modules/nf-core/gawk/environment.yml pypi
modules/nf-core/gnu/sort/environment.yml pypi
modules/nf-core/tabix/bgziptabix/environment.yml pypi