fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 10 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
1 of 28 committers (3.6%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary

Keywords

ddbj download ena fastq geo nextflow nf-core pipeline sra synapse workflow

Keywords from Contributors

workflows pipelines nf-test dsl2 metagenomics taxonomic-classifications taxonomic-profiling atac-seq chromatin-accessibiity illumina

Last synced: 6 months ago · JSON representation ·

Repository

Pipeline to fetch metadata and raw FastQ files from public databases

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: master
Homepage: https://nf-co.re/fetchngs
Size: 4.42 MB

Statistics

Stars: 177
Watchers: 116
Forks: 81
Open Issues: 43
Releases: 14

Topics

ddbj download ena fastq geo nextflow nf-core pipeline sra synapse workflow

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/fetchngs is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO ids (see usage docs).

nf-core/fetchngs metro map

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:

ids.csv:

csv SRR9984183 SRR13191702 ERR1160846 ERR1109373 DRR028935 DRR026872

Each line represents a database id. Please see next section for supported ids.

Now, you can run the pipeline using:

bash nextflow run nf-core/fetchngs \ -profile <docker/singularity/.../institute> \ --input ids.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.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Supported ids

Via a single file of ids, provided one-per-line (see example input file) the pipeline performs the following steps:

SRA / ENA / DDBJ / GEO ids

Resolve database ids back to appropriate experiment-level ids and to be compatible with the ENA API
Fetch extensive id metadata via ENA API
Download FastQ files:
- If direct download links are available from the ENA API:
  - Fetch in parallel via wget and perform md5sum check (--download_method ftp; default).
  - Fetch in parallel via aspera-cli and perform md5sum check. Use --download_method aspera to force this behaviour.
- Otherwise use sra-tools to download .sra files and convert them to FastQ. Use --download_method sratools to force this behaviour.
Collate id metadata and paths to FastQ files in a single samplesheet

Pipeline output

The columns in the output samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines (see usage docs), these currently include:

nf-core/rnaseq
nf-core/atacseq
Ilumina processing mode of nf-core/viralrecon
nf-core/taxprofiler

To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

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.

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #fetchngs channel (you can join with this invite).

Citations

If you use nf-core/fetchngs for your analysis, please cite it using the following doi: 10.5281/zenodo.5070524

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

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: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

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.

GitHub Events

Total

Issues event: 10
Watch event: 28
Delete event: 8
Issue comment event: 49
Push event: 46
Pull request review event: 41
Pull request review comment event: 35
Pull request event: 29
Fork event: 13
Create event: 12

Last Year

Issues event: 10
Watch event: 28
Delete event: 8
Issue comment event: 49
Push event: 46
Pull request review event: 41
Pull request review comment event: 35
Pull request event: 29
Fork event: 13
Create event: 12

Committers

Last synced: over 2 years ago

All Time

Total Commits: 599
Total Committers: 28
Avg Commits per committer: 21.393
Development Distribution Score (DDS): 0.661

Past Year

Commits: 371
Committers: 19
Avg Commits per committer: 19.526
Development Distribution Score (DDS): 0.671

Top Committers

Name	Email	Commits
Harshil Patel	d**h@g**m	203
maxulysse	m**a@g**m	122
Sateesh Peri	p**h@g**m	48
Adam Talbot	1****t	38
Moritz E. Beber	m**r@p**t	38
Maxime U Garcia	m**a@s**o	27
ejseqera	e**i@s**o	23
Harshil Patel	d****h	22
Daisy Wenyan Han	6****7	20
nf-core-bot	c**e@n**e	15
Jonathan Manning	j**g@h**o	9
James Fellows Yates	j**3@g**m	5
Sateesh_Peri	3****i	4
Esha Joshi	e**i@e**e	3
Rob Syme	r**e@g**m	3
Edmund Miller	e**r@p**m	3
Esha Joshi	1****a	3
davidecarlson	d**n@s**u	2
maxibor	m**y@g**m	2
jahdoos	r**0@g**m	1
kevinmenden	k**n@t**e	1
MCMandR	1****R	1
Oliver Ziff	4****f	1
Phil Ewels	p**s@s**e	1
Adam Talbot	a**t@s**o	1
Alain Domissy	a**y@g**m	1
sirclockalot	l**y@g**m	1
EC2 Default User	e**r@i**l	1

Committer Domains (Top 20 + Academic)

seqera.io: 3 ip-172-31-58-117.ec2.internal: 1 scilifelab.se: 1 t-online.de: 1 stonybrook.edu: 1 eshas-mbp.home: 1 healx.io: 1 nf-co.re: 1 posteo.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 61
Total pull requests: 127
Average time to close issues: 4 months
Average time to close pull requests: 12 days
Total issue authors: 44
Total pull request authors: 25
Average comments per issue: 2.59
Average comments per pull request: 1.7
Merged pull requests: 97
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 15
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Issue authors: 7
Pull request authors: 9
Average comments per issue: 0.0
Average comments per pull request: 0.53
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

drpatelh (7)
dmalzl (5)
pinin4fjords (3)
ojziff (3)
suhrig (2)
lindenb (2)
maxulysse (2)
millerh1 (2)
jfy133 (2)
telatin (2)
el239 (2)
Midnighter (2)
alexblaessle (2)
awalsh17 (1)
tanaes (1)

Pull Request Authors

drpatelh (43)
maxulysse (40)
adamrtalbot (28)
nf-core-bot (28)
sateeshperi (9)
bentsherman (8)
ejseqera (4)
robsyme (3)
suhrig (3)
edmundmiller (3)
pinin4fjords (2)
Midnighter (2)
vsmalladi (2)
maxibor (2)
Emiller88 (1)

Top Labels

Issue Labels

bug (43) enhancement (29) documentation (1)

Pull Request Labels

enhancement (4) bug (2)

Dependencies

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v3 composite
actions/checkout v2 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

.github/workflows/clean-up.yml actions

actions/stale v7 composite

.github/workflows/cloud_tests_full.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

.github/workflows/cloud_tests_small.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

modules/nf-core/custom/sratoolsncbisettings/meta.yml cpan

modules/nf-core/sratools/fasterqdump/meta.yml cpan

modules/nf-core/sratools/prefetch/meta.yml cpan

subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml cpan

pyproject.toml pypi

.github/workflows/release-announcments.yml actions

actions/setup-python v4 composite
rzr/fediverse-action master composite
zentered/bluesky-post-action v0.0.2 composite

modules/nf-core/untar/meta.yml cpan

subworkflows/nf-core/nextflowpipelineutils/meta.yml cpan

subworkflows/nf-core/nfcore_pipeline_utils/meta.yml cpan

subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml cpan

fetchngs

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Introduction

Usage

Supported ids

SRA / ENA / DDBJ / GEO ids

Pipeline output

Credits

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies