sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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

Science Score: 67.0%

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Keywords

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Keywords from Contributors

pipelines workflows dsl2 nf-test metagenomes rna-seq rna illumina epigenome 10xgenomics

Last synced: 4 months ago · JSON representation ·

Repository

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: master
Homepage: https://nf-co.re/sarek
Size: 107 MB

Statistics

Stars: 473
Watchers: 149
Forks: 472
Open Issues: 336
Releases: 28

Topics

Created over 6 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codeowners

README.md

Introduction

nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

It's listed on Elixir - Tools and Data Services Registry and Dockstore.

Sarek Workflow

Pipeline summary

Depending on the options and samples provided, the pipeline can currently perform the following:

Form consensus reads from UMI sequences (fgbio)
Sequencing quality control and trimming (enabled by --trim_fastq) (FastQC, fastp)
Map Reads to Reference (BWA-mem, BWA-mem2, dragmap or Sentieon BWA-mem)
Process BAM file (GATK MarkDuplicates, GATK BaseRecalibrator and GATK ApplyBQSR or Sentieon LocusCollector and Sentieon Dedup)
Summarise alignment statistics (samtools stats, mosdepth)
Variant calling (enabled by --tools, see compatibility):
- ASCAT
- CNVkit
- Control-FREEC
- DeepVariant
- freebayes
- GATK HaplotypeCaller
- Manta
- indexcov
- mpileup
- MSIsensor-pro
- Mutect2
- Sentieon Haplotyper
- Strelka2
- TIDDIT
- Lofreq
Variant filtering and annotation (SnpEff, Ensembl VEP, BCFtools annotate)
Summarise and represent QC (MultiQC)

Sarek Workflow

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:

samplesheet.csv:

csv patient,sample,lane,fastq_1,fastq_2 ID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz

Each row represents a pair of fastq files (paired end).

Now, you can run the pipeline using:

bash nextflow run nf-core/sarek \ -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.

Benchmarking

On each release, the pipeline is run on 3 full size tests:

test_full runs tumor-normal data for one patient from the SEQ2C consortium
test_full_germline runs a WGS 30X Genome-in-a-Bottle(NA12878) dataset
test_full_germline_ncbench_agilent runs two WES samples with 75M and 200M reads (data available here). The results are uploaded to Zenodo, evaluated against a truth dataset, and results are made available via the NCBench dashboard.

Credits

Sarek was originally written by Maxime U Garcia and Szilveszter Juhos at the National Genomics Infastructure and National Bioinformatics Infastructure Sweden which are both platforms at SciLifeLab, with the support of The Swedish Childhood Tumor Biobank (Barntumörbanken). Friederike Hanssen and Gisela Gabernet at QBiC later joined and helped with further development.

The Nextflow DSL2 conversion of the pipeline was lead by Friederike Hanssen and Maxime U Garcia.

Maintenance is now lead by Friederike Hanssen and Maxime U Garcia (now at Seqera Labs)

Main developers:

We thank the following people for their extensive assistance in the development of this pipeline:

Acknowledgements

| | | | :-----------------------------------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------: | | | | | | | | | |

Contributions & 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 #sarek channel (you can join with this invite), or contact us: Maxime U Garcia, Friederike Hanssen

Citations

If you use nf-core/sarek for your analysis, please cite the Sarek article as follows:

Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery NAR Genomics and Bioinformatics Volume 6, Issue 2, June 2024, lqae031, doi: 10.1093/nargab/lqae031.

Garcia M, Juhos S, Larsson M et al. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved] F1000Research 2020, 9:63 doi: 10.12688/f1000research.16665.2.

You can cite the sarek zenodo record for a specific version using the following doi: 10.5281/zenodo.3476425

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.

CHANGELOG

CHANGELOG

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/sarek: Citations

## [nf-core/sarek 3](https://www.biorxiv.org/content/10.1101/2023.07.19.549462v2)

> Hanssen F, Garcia MU, Folkersen L, Pedersen AS, Lescai F, Jodoin S, Miller E, Wacker O, Smith N, nf-core community, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. bioRxiv. 2023 Jul 19:2023-07.

## [nf-core/sarek](https://pubmed.ncbi.nlm.nih.gov/32269765/)

> Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels PA, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res. 2020 Jan 29;9:63. eCollection 2020. doi: 10.12688/f1000research.16665.2. PubMed PMID: 32269765.

## [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

- [ASCAT](https://pubmed.ncbi.nlm.nih.gov/20837533/)

  > Van Loo P, Nordgard SH, Lingjærde OC, et al.: Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA . 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. PubMed PMID: 20837533; PubMed Central PMCID: PMC2947907.

- [alleleCount](https://github.com/cancerit/alleleCount)

- [BCFTools](https://pubmed.ncbi.nlm.nih.gov/21903627/)

  > Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575.

- [BGZip](https://github.com/madler/pigz)

- [BWA-MEM](https://arxiv.org/abs/1303.3997v2)

  > Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013. doi: 10.48550/arXiv.1303.3997

- [BWA-MEM2](https://ieeexplore.ieee.org/document/8820962)

  > M. Vasimuddin, S. Misra, H. Li and S. Aluru, "Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems," 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2019, pp. 314-324. doi: 10.1109/IPDPS.2019.00041.

- [CNVKIT](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873)

  > Talevich E, Shain AH, Botton T, Bastian BC (2016) CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol 12(4): e1004873. doi: 10.1371/journal.pcbi.1004873. PubMed PMID: 27100738. PubMed Central PMCID: PMC4839673.

- [Control-FREEC](https://pubmed.ncbi.nlm.nih.gov/22155870/)

  > Boeva V, Popova T, Bleakley K, et al.: Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics. 2012; 28(3): 423–5. doi: 10.1093/bioinformatics/btr670. Epub 2011 Dec 6. PubMed PMID: 22155870; PubMed Central PMCID: PMC3268243.

- [dbNSFP](https://pubmed.ncbi.nlm.nih.gov/33261662/)

  > Liu X, et al.: dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Med. 2020 Dec 2;12(1):103. doi: 10.1186/s13073-020-00803-9. PubMed PMID: 33261662; PubMed Central PMCID: PMC7709417.

- [DeepVariant](https://www.nature.com/articles/nbt.4235)

  > Poplin, R., Chang, PC., Alexander, D. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36, 983–987 (2018). doi: 10.1038/nbt.4235.

- [DragMap](https://github.com/Illumina/DRAGMAP)

- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/)

  > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825.

- [FastP](https://academic.oup.com/bioinformatics/article/34/17/i884/5093234)

  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086. PubMed Central PMCID: PMC6129281

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [FGBio](https://github.com/fulcrumgenomics/fgbio)

  > doi: 10.5281/zenodo.10456900

- [FreeBayes](https://arxiv.org/abs/1207.3907)

  > Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012. doi: 10.48550/arXiv.1207.3907

- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/)

  > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.

- [GNU sed](http://www.gnu.org/software/sed/)

- [HaplotypeCaller Joint Germline](https://www.biorxiv.org/content/10.1101/201178v3)

  > Poplin R. et al, Scaling accurate genetic variant discovery to tens of thousands of samples, bioRxiv 2018. doi: 10.1101/201178

- [LOFTEE](https://pubmed.ncbi.nlm.nih.gov/32461654/)

  > Karczewski KJ, et al.: The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. doi: 10.1038/s41586-020-2308-7. PubMed PMID: 32461654; PubMed Central PMCID: PMC7334197.

- [Manta](https://pubmed.ncbi.nlm.nih.gov/26647377/)

  > Chen X, Schulz-Trieglaff O, Shaw R, et al.: Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. PubMed PMID: 26647377.

- [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630)

  > Brent S Pedersen, Aaron R Quinlan, Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34, Issue 5, 01 March 2018, Pages 867–868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012. PubMed Central PMCID: PMC6030888.

- [MSISensorPro](https://www.sciencedirect.com/science/article/pii/S1672022920300218)

  > Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020,18(1). doi: 10.1016/j.gpb.2020.02.001. PubMed PMID: 32171661. PubMed Central PMCID: PMC7393535.

- [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.

- [PIGZ](https://zlib.net/pigz/)

- [P7Zip](http://p7zip.sourceforge.net/)

- [Samblaster](https://academic.oup.com/bioinformatics/article/30/17/2503/2748175)

  > Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction, Bioinformatics, Volume 30, Issue 17, 1 September 2014, Pages 2503–2505. doi: 10.1093/bioinformatics/btu314. PubMed PMID: 24812344. PubMed Central PMCID: PMC4147885.

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [snpEff](https://pubmed.ncbi.nlm.nih.gov/22728672/)

  > Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285.

- [SpliceAI](https://pubmed.ncbi.nlm.nih.gov/30661751/)

  > Jaganathan K, et al.: Predicting Splicing from Primary Sequence with Deep Learning. Cell. 2019 Jan 24;176(3):535-548.e24. doi: 10.1016/j.cell.2018.12.015. PubMed PMID: 30661751.

- [SpliceRegion](https://github.com/Ensembl/VEP_plugins/blob/release/106/SpliceRegion.pm)

- [Strelka2](https://pubmed.ncbi.nlm.nih.gov/30013048/)

  > Kim S, Scheffler K, Halpern AL, et al.: Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods. 2018 Aug;15(8):591-594. doi: 10.1038/s41592-018-0051-x. Epub 2018 Jul 16. PubMed PMID: 30013048.

- [SVDB](https://github.com/J35P312/SVDB)

- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)

  > Li H, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982. PubMed Central PMCID: PMC3042176.

- [TIDDIT](https://pubmed.ncbi.nlm.nih.gov/28781756/)

  > Eisfeldt J, Vezzi F, Olason P, et al.: TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017 May 10;6:664. doi: 10.12688/f1000research.11168.2. eCollection 2017. PubMed PMID: 28781756; PubMed Central PMCID: PMC5521161.

- [VCFTools](https://pubmed.ncbi.nlm.nih.gov/21653522/)

  > Danecek P, Auton A, Abecasis G, et al.: The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. PubMed PMID: 21653522; PubMed Central PMCID: PMC3137218.

- [Lofreq](https://pubmed.ncbi.nlm.nih.gov/23066108/)

  > Wilm et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40(22):11189-201.

## R packages

- [R](https://www.R-project.org/)

  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)

  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.

## 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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Create event: 34
Commit comment event: 2
Release event: 2
Issues event: 149
Watch event: 71
Delete event: 28
Issue comment event: 635
Push event: 328
Pull request event: 242
Pull request review event: 618
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Fork event: 69

Committers

Last synced: almost 2 years ago

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Total Commits: 5,415
Total Committers: 69
Avg Commits per committer: 78.478
Development Distribution Score (DDS): 0.572

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Commits: 1,421
Committers: 32
Avg Commits per committer: 44.406
Development Distribution Score (DDS): 0.595

Top Committers

Name	Email	Commits
MaxUlysse	m**a@g**m	2,316
Rike	f**n@q**e	1,317
Anders Sune Pedersen	a**e@c**k	237
asp8200	a**s@m**m	184
FriederikeHanssen	F**n@q**e	181
ggabernet	g**t@q**e	136
SusiJo	s**n@g**e	106
WackerO	o**r@w**e	91
Smith Nicholas	s**h@i**e	79
Adam Talbot	1****t	60
Maxime U. Garcia	m**a@s**e	60
Anders Sune Pedersen	3****0	53
jfnavarro	j**o@g**m	47
nf-core-bot	c**e@n**e	46
nickhsmith	s**h@g**m	45
Chela James	c**s@i**k	45
Bekir Erguner	b**r@e**k	34
Alexander Peltzer	a**r@g**m	31
Edmund Miller	e**r@p**m	29
mirpedrol	m**a@g**m	29
Simon Pearce	2****e	23
Grant Neilson	g**t@c**m	22
WackerO	4****O	18
Bekir Ergüner	b**e@g**m	18
Chela James	c**k@y**k	16
Malin Larsson	m**n@l**e	15
Francesco	l**i@b**k	13
Malin Larsson	m****n	11
David Mas-Ponte	d**p@g**m	10
Adam Talbot	a**t@s**o	10
and 39 more...

Committer Domains (Top 20 + Academic)

qbic.uni-tuebingen.de: 3 scilifelab.se: 3 seqera.io: 2 cam.ac.uk: 1 clin.au.dk: 1 mynucleus.com: 1 gmx.de: 1 in.tum.de: 1 nibsc.org: 1 nf-co.re: 1 icr.ac.uk: 1 exscientia.co.uk: 1 cosyne.com: 1 yahoo.co.uk: 1 liu.se: 1 biomed.au.dk: 1 t-online.de: 1 rddsws.am10.uni-tuebingen.de: 1 igmm.ed.ac.uk: 1 me.com: 1 ucl.ac.uk: 1 ed.ac.uk: 1

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Dependencies

.github/workflows/awstest.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v2 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

Wandalen/wretry.action v1 composite
actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v2 composite
conda-incubator/setup-miniconda v2 composite
dorny/paths-filter v2 composite
eWaterCycle/setup-singularity v5 composite
nf-core/setup-nextflow v1 composite

.github/workflows/clean-up.yml actions

actions/stale v7 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/ascat/meta.yml cpan

modules/nf-core/bcftools/concat/meta.yml cpan

modules/nf-core/bcftools/mpileup/meta.yml cpan

modules/nf-core/bcftools/sort/meta.yml cpan

modules/nf-core/bcftools/stats/meta.yml cpan

modules/nf-core/bwa/index/meta.yml cpan

modules/nf-core/bwa/mem/meta.yml cpan

modules/nf-core/bwamem2/index/meta.yml cpan

modules/nf-core/bwamem2/mem/meta.yml cpan

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

modules/nf-core/cat/fastq/meta.yml cpan

modules/nf-core/cnvkit/antitarget/meta.yml cpan

modules/nf-core/cnvkit/batch/meta.yml cpan

modules/nf-core/cnvkit/reference/meta.yml cpan

modules/nf-core/controlfreec/assesssignificance/meta.yml cpan

modules/nf-core/controlfreec/freec/meta.yml cpan

modules/nf-core/controlfreec/freec2bed/meta.yml cpan

modules/nf-core/controlfreec/freec2circos/meta.yml cpan

modules/nf-core/controlfreec/makegraph/meta.yml cpan

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

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

modules/nf-core/dragmap/align/meta.yml cpan

modules/nf-core/dragmap/hashtable/meta.yml cpan

modules/nf-core/ensemblvep/download/meta.yml cpan

modules/nf-core/ensemblvep/vep/meta.yml cpan

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

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

modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml cpan

modules/nf-core/fgbio/fastqtobam/meta.yml cpan

modules/nf-core/fgbio/groupreadsbyumi/meta.yml cpan

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

modules/nf-core/gatk4/applybqsr/meta.yml cpan

modules/nf-core/gatk4/applybqsrspark/meta.yml cpan

modules/nf-core/gatk4/applyvqsr/meta.yml cpan

modules/nf-core/gatk4/baserecalibrator/meta.yml cpan

modules/nf-core/gatk4/baserecalibratorspark/meta.yml cpan

modules/nf-core/gatk4/calculatecontamination/meta.yml cpan

modules/nf-core/gatk4/cnnscorevariants/meta.yml cpan

modules/nf-core/gatk4/createsequencedictionary/meta.yml cpan

modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml cpan

modules/nf-core/gatk4/filtermutectcalls/meta.yml cpan

modules/nf-core/gatk4/filtervarianttranches/meta.yml cpan

modules/nf-core/gatk4/gatherbqsrreports/meta.yml cpan

modules/nf-core/gatk4/gatherpileupsummaries/meta.yml cpan

modules/nf-core/gatk4/genomicsdbimport/meta.yml cpan

modules/nf-core/gatk4/genotypegvcfs/meta.yml cpan

modules/nf-core/gatk4/getpileupsummaries/meta.yml cpan

modules/nf-core/gatk4/haplotypecaller/meta.yml cpan

modules/nf-core/gatk4/intervallisttobed/meta.yml cpan

modules/nf-core/gatk4/learnreadorientationmodel/meta.yml cpan

modules/nf-core/gatk4/markduplicates/meta.yml cpan

modules/nf-core/gatk4/markduplicatesspark/meta.yml cpan

modules/nf-core/gatk4/mergemutectstats/meta.yml cpan

modules/nf-core/gatk4/mergevcfs/meta.yml cpan

modules/nf-core/gatk4/mutect2/meta.yml cpan

modules/nf-core/gatk4/variantrecalibrator/meta.yml cpan

modules/nf-core/manta/germline/meta.yml cpan

modules/nf-core/manta/somatic/meta.yml cpan

modules/nf-core/manta/tumoronly/meta.yml cpan

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

modules/nf-core/msisensorpro/msisomatic/meta.yml cpan

modules/nf-core/msisensorpro/scan/meta.yml cpan

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

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

modules/nf-core/samtools/bam2fq/meta.yml cpan

modules/nf-core/samtools/collatefastq/meta.yml cpan

modules/nf-core/samtools/convert/meta.yml cpan

modules/nf-core/samtools/faidx/meta.yml cpan

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modules/nf-core/samtools/view/meta.yml cpan

modules/nf-core/sentieon/applyvarcal/meta.yml cpan

modules/nf-core/sentieon/bwamem/meta.yml cpan

modules/nf-core/sentieon/dedup/meta.yml cpan

modules/nf-core/sentieon/gvcftyper/meta.yml cpan

modules/nf-core/sentieon/haplotyper/meta.yml cpan

modules/nf-core/sentieon/varcal/meta.yml cpan

modules/nf-core/snpeff/download/meta.yml cpan

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

modules/nf-core/strelka/germline/meta.yml cpan

modules/nf-core/strelka/somatic/meta.yml cpan

modules/nf-core/svdb/merge/meta.yml cpan

modules/nf-core/tabix/bgziptabix/meta.yml cpan

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

modules/nf-core/tiddit/sv/meta.yml cpan

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

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

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

subworkflows/local/bam_joint_calling_germline_gatk/meta.yml cpan

subworkflows/local/bam_variant_calling_somatic_mutect2/meta.yml cpan

subworkflows/local/bam_variant_calling_tumor_only_mutect2/meta.yml cpan