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reproduce-nf-core-fetchngs

https://github.com/arwisyah/reproduce-nf-core-fetchngs

Science Score: 44.0%

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Repository

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  • Host: GitHub
  • Owner: arwisyah
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Size: 6.74 MB
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  • Watchers: 1
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  • Open Issues: 0
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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/fetchngs Workflow on Gitpod

This guide will walk you through setting up and running the nf-core/fetchngs Nextflow workflow on Gitpod using the sratools download method.

Prerequisites

  1. Gitpod Account: Make sure you have an account on Gitpod.
  2. Fork the Repository: Fork the nf-core/fetchngs repository to your GitHub workspace.

Setup

  1. Launch Gitpod: Open your forked repository on GitHub and click the Gitpod button to launch a new workspace.

  2. Verify Nextflow Installation: Ensure Nextflow is installed and working. Run the following command in the Gitpod terminal: sh nextflow info You should see output similar to: Version: 24.04.2 build 5914 Created: 29-05-2024 06:19 UTC System: Linux 6.1.89-060189-generic Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.11-internal+0-adhoc..src Encoding: UTF-8 (UTF-8)

Running the Workflow

  1. Create the Input File: Create an ids.csv file with the database IDs. Each line represents a database ID.

sh echo -e "SRR9984183\nSRR13191702\nERR1160846\nERR1109373\nDRR028935\nDRR026872" > ids.csv

  1. Run the Workflow: Execute the fetchngs workflow using Nextflow with the sratools download method. sh nextflow run nf-core/fetchngs -profile docker --input ids.csv --outdir output --download_method sratools

Verifying the Output

  1. Check the Output Directory: Verify that the output files have been downloaded and processed correctly.

sh ls output

  1. Review Logs: Optionally, review the logs for any warnings or important messages. sh find work -name '.command.log' -exec cat {} \;

Using the Output

The output generated by nf-core/fetchngs can be seamlessly used as input for the following workflows:

Note : in original workflow, the output can also be used on nf-core/taxprofiler. However, the link of the workflow is no longer exist.

As an example, To use the output of nf-core/fetchngs with nf-core/rnaseq, follow these steps:

  1. Modify Samplesheet.csv: Add a new column named strandedness to the samplesheet.csv file with the value "auto" for all samples. This ensures that the strandedness of RNA-seq libraries will be automatically detected during the analysis.

  2. Run nf-core/rnaseq: Execute the nf-core/rnaseq workflow with the modified samplesheet.csv file as input.

sh nextflow run nf-core/rnaseq \ --input /path/to/modified/samplesheet.csv \ --outdir /path/to/rnaseq_output \ --genome GRCh37 \ -profile docker

Replace /path/to/modified/samplesheet.csv with the path to your modified samplesheet.csv file and /path/to/rnaseq_output with the desired output directory.

For other workflows, you can check on how to modified samplesheet.csv from the hyperlink above.

Citations

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.

Conclusion

By following these steps, you should be able to successfully run the nf-core/fetchngs workflow on Gitpod using the sratools download method. Ensure you review the outputs and logs to verify that the workflow has completed as expected.

Credits

nf-core/fetchngs was originally written by Harshil Patel (@drpatelh) from Seqera Labs, Spain and Jose Espinosa-Carrasco (@JoseEspinosa) from The Comparative Bioinformatics Group at The Centre for Genomic Regulation, Spain. Support for download of sequencing reads without FTP links via sra-tools was added by Moritz E. Beber (@Midnighter) from Unseen Bio ApS, Denmark.

Owner

  • Name: Arya Wira Syahdwinata
  • Login: arwisyah
  • Kind: user
  • Location: Bekasi Regency, Indonesia

Currently working on Data Analytics and Machine Learning Projects

Citation (CITATIONS.md) 

# nf-core/fetchngs: 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

- [Aspera CLI](https://github.com/IBM/aspera-cli)

- [Python](http://www.python.org)

- [Requests](https://docs.python-requests.org/)

- [sra-tools](https://github.com/ncbi/sra-tools)

## Pipeline resources

- [ENA](https://pubmed.ncbi.nlm.nih.gov/33175160/)

  > Harrison PW, Ahamed A, Aslam R, Alako BTF, Burgin J, Buso N, Courtot M, Fan J, Gupta D, Haseeb M, Holt S, Ibrahim T, Ivanov E, Jayathilaka S, Kadhirvelu VB, Kumar M, Lopez R, Kay S, Leinonen R, Liu X, O'Cathail C, Pakseresht A, Park Y, Pesant S, Rahman N, Rajan J, Sokolov A, Vijayaraja S, Waheed Z, Zyoud A, Burdett T, Cochrane G. The European Nucleotide Archive in 2020. Nucleic Acids Res. 2021 Jan 8;49(D1):D82-D85. doi: 10.1093/nar/gkaa1028. PubMed PMID: 33175160; PubMed Central PMCID: PMC7778925.

- [SRA](https://pubmed.ncbi.nlm.nih.gov/21062823/)

  > Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011 Jan;39 (Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9. PubMed PMID: 21062823; PubMed Central PMCID: PMC3013647.

- [DDBJ](https://pubmed.ncbi.nlm.nih.gov/33156332/)

  > Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O. DDBJ update: streamlining submission and access of human data. Nucleic Acids Res. 2021 Jan 8;49(D1):D71-D75. doi: 10.1093/nar/gkaa982. PubMed PMID: 33156332; PubMed Central PMCID: PMC7779041.

- [GEO](https://pubmed.ncbi.nlm.nih.gov/23193258/)

  > Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5. doi: 10.1093/nar/gks1193. Epub 2012 Nov 27. PubMed PMID: 23193258; PubMed Central PMCID: PMC3531084.

## Software packaging/containerisation/testing 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.

- [nf-test](https://code.askimed.com/nf-test)

- [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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