testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.

https://github.com/nf-core/testpipeline

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
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
2 of 10 committers (20.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary

Keywords from Contributors

nextflow nf-core workflows pipelines bioinformatics atac-seq chromatin-accessibiity nf-test dsl2 long-read-sequencing

Last synced: 6 months ago · JSON representation ·

Repository

A small example pipeline used to test new nf-core infrastructure and common code.

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: main
Size: 3.24 MB

Statistics

Stars: 5
Watchers: 7
Forks: 42
Open Issues: 12
Releases: 0

Created over 5 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/testpipeline is a bioinformatics pipeline that ...

1. Read QC (FastQC)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 nf-core/testpipeline \ -profile <docker/singularity/.../institute> \ --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.

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

Pipeline output

To see the results of an example 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/testpipeline was originally written by nf-core.

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.

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

Citations

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.

this is a test

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/testpipeline: 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].

- [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

Total

Watch event: 1
Delete event: 29
Issue comment event: 14
Push event: 51
Pull request review comment event: 4
Pull request review event: 9
Pull request event: 50
Fork event: 3
Create event: 18

Last Year

Watch event: 1
Delete event: 29
Issue comment event: 14
Push event: 51
Pull request review comment event: 4
Pull request review event: 9
Pull request event: 50
Fork event: 3
Create event: 18

Committers

Last synced: over 2 years ago

All Time

Total Commits: 109
Total Committers: 10
Avg Commits per committer: 10.9
Development Distribution Score (DDS): 0.679

Past Year

Commits: 39
Committers: 8
Avg Commits per committer: 4.875
Development Distribution Score (DDS): 0.641

Top Committers

Name	Email	Commits
ggabernet	g**t@q**e	35
Rike	f**n@q**e	34
mirpedrol	m**a@g**m	14
Matthias Hörtenhuber	m**3@g**m	8
Matthias Hörtenhuber	m****u	5
Phil Ewels	p**s@s**e	5
Rob Syme	r**e@g**m	4
nf-core-bot	c**e@n**e	2
nicolasDelhomme	n**e@u**e	1
Phil Ewels	p**l@s**o	1

Committer Domains (Top 20 + Academic)

qbic.uni-tuebingen.de: 2 seqera.io: 1 umu.se: 1 nf-co.re: 1 scilifelab.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 2
Total pull requests: 87
Average time to close issues: 4 months
Average time to close pull requests: 9 days
Total issue authors: 2
Total pull request authors: 13
Average comments per issue: 0.5
Average comments per pull request: 1.14
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 19
Average time to close issues: 13 minutes
Average time to close pull requests: 1 day
Issue authors: 1
Pull request authors: 4
Average comments per issue: 0.0
Average comments per pull request: 0.42
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

tgbrooks (1)
mirpedrol (1)

Pull Request Authors

nf-core-bot (38)
mirpedrol (30)
ewels (11)
ggabernet (7)
KevinMenden (5)
gq1 (4)
mashehu (3)
robsyme (3)
FriederikeHanssen (2)
jfy133 (1)
nvnieuwk (1)
maxulysse (1)
apeltzer (1)

Top Labels

Issue Labels

bug (1)

Pull Request Labels

Dependencies

.github/workflows/download.yml actions

actions/setup-python v3 composite
eWaterCycle/setup-singularity v7 composite
nf-core/setup-nextflow v1 composite

.github/workflows/awsfulltest.yml actions

nf-core/tower-action main composite

.github/workflows/awstest.yml actions

nf-core/tower-action main composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite
nf-core/setup-nextflow v1 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v2 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
actions/setup-node v2 composite
actions/setup-python v3 composite
actions/upload-artifact v2 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/release-announcments.yml actions

actions/setup-python v4 composite
rzr/fediverse-action master composite

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

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

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

pyproject.toml pypi

testpipeline

Science Score: 67.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

Introduction

Usage

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