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nascent

Nascent Transcription Processing Pipeline

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

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
    4 of 17 committers (23.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary

Keywords

gro-seq nascent nextflow nf-core pipeline pro-seq rna transcription tss workflow

Keywords from Contributors

taxonomic-profiling taxonomic-classification rrna qiime2 pacbio microbiome metagenomics metabarcoding its iontorrent
Last synced: 6 months ago · JSON representation ·

Repository

Nascent Transcription Processing Pipeline

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage: https://nf-co.re/nascent
  • Size: 8.8 MB
Statistics
  • Stars: 19
  • Watchers: 170
  • Forks: 11
  • Open Issues: 56
  • Releases: 6
Topics
gro-seq nascent nextflow nf-core pipeline pro-seq rna transcription tss workflow
Created over 7 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/nascent

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

nf-core/nascent is a bioinformatics best-practice analysis pipeline for nascent transcript (NT) and Transcriptional Start Site (TSS) assays.

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.

Pipeline summary

  1. Read QC (FastQC)
  2. Adapter and quality trimming (fastp)
  3. Alignment
    1. bwa
    2. bwamem2
    3. DRAGMAP
  4. Sort and index alignments (SAMtools)
  5. UMI-based deduplication (UMI-tools)
  6. Duplicate read marking (picard MarkDuplicates)
  7. Quality Control
    1. RSeQC - Various RNA-seq QC metrics
    2. Preseq - Estimation of library complexity
    3. BBMap - Analyzes the sequencing coverage
  8. Coverage Graphs
    1. Create bedGraph coverage files (BEDTools
    2. Create bigWig coverage files (deeptools)
  9. Transcript identification
    1. HOMER
    2. GroHMM
    3. PINTS
  10. Quantification of Genes and Nascent Transcripts (featureCounts)
  11. Aggregate report describing results and QC from the whole pipeline (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/nascent \ -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/nascent was originally written by Ignacio Tripodi (@ignaciot) and Margaret Gruca (@magruca).

The pipeline was re-written in Nextflow DSL2 by Edmund Miller (@edmundmiller) and Sruthi Suresh (@sruthipsuresh) from The Functional Genomics Laboratory at The Univeristy of Texas at Dallas

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 #nascent channel (you can join with this invite).

Citations

If you use nf-core/nascent for your analysis, please cite it using the following doi: 10.5281/zenodo.7245273

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

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

Citation (CITATIONS.md) 

# nf-core/nascent: 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

- [BBMap](https://sourceforge.net/projects/bbmap/)

- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

- [Bowtie 2](https://www.nature.com/articles/nmeth.1923)

  > Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). doi: 10.1038/nmeth.1923.

- [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.

- [deepTools](https://github.com/deeptools/deepTools)

  > Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257.

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

- [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].

- [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.

- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)

  > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.

- [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)

  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.

- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)

  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.

- [HOMER](http://homer.ucsd.edu/homer/index.html)

  > Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

- [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.

- [PINTS](https://pints.yulab.org/)

  > Yao, L., Liang, J., Ozer, A. et al. A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. Nat Biotechnol 40, 1056–1065 (2022). https://doi.org/10.1038/s41587-022-01211-7

- [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)

  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.

- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)

  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.

- [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.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)

  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.

## Python packages

- [Pandas](https://pandas.pydata.org/about/citing.html)

  > The pandas development team. (2022). pandas-dev/pandas: Pandas (v1.5.2). Zenodo. doi: 10.5281/zenodo.3509134

## 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.

- [argparse](https://cran.r-project.org/package=argparse)

- [GenomicAlignments](https://bioconductor.org/packages/GenomicAlignments/)

  > Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M, Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9. doi: 10.1371/journal.pcbi.1003118, http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118.

- [GenomicFeatures](https://www.bioconductor.org/packages/GenomicFeatures/)

  > Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M, Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9. doi: 10.1371/journal.pcbi.1003118, http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118.

- [groHMM](https://www.bioconductor.org/packages/groHMM/)

  > Chae M, Danko CG, Kraus WL (2015). “groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.” BMC Bioinformatics, 16(222).

## 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
  • Create event: 21
  • Release event: 1
  • Issues event: 25
  • Watch event: 1
  • Delete event: 16
  • Issue comment event: 38
  • Push event: 173
  • Pull request review event: 51
  • Pull request review comment event: 35
  • Pull request event: 35
Last Year
  • Create event: 21
  • Release event: 1
  • Issues event: 25
  • Watch event: 1
  • Delete event: 16
  • Issue comment event: 38
  • Push event: 173
  • Pull request review event: 51
  • Pull request review comment event: 35
  • Pull request event: 35

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 947
  • Total Committers: 17
  • Avg Commits per committer: 55.706
  • Development Distribution Score (DDS): 0.271
Past Year
  • Commits: 221
  • Committers: 5
  • Avg Commits per committer: 44.2
  • Development Distribution Score (DDS): 0.054
Top Committers
Name Email Commits
Edmund Miller e****r@p****m 690
Edmund Miller e****r@g****m 105
Ignacio Tripodi i****i@c****u 38
sruthipsuresh s****h@g****m 25
nf-core-bot c****e@n****e 22
Sruthi Suresh s****4@g****u 22
Alexander Peltzer a****r@g****m 14
Ignacio Tripodi i****t@g****m 10
sruthipsuresh 5****h@u****m 7
Edmund E****r@g****m 3
Nithya Jaisankar n****6@g****u 3
Margaret Gruca m****a@c****u 2
Alexander Peltzer a****r@u****m 2
kevinmenden k****n@t****e 1
runner r****r@f****0 1
Ignacio Tripodi i****t@u****m 1
nithyaj12 n****2@g****m 1
Committer Domains (Top 20 + Academic)
ganymede.utdallas.edu: 2 colorado.edu: 2 t-online.de: 1 nf-co.re: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 69
  • Total pull requests: 67
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 0.62
  • Average comments per pull request: 1.39
  • Merged pull requests: 36
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 17
  • Pull requests: 7
  • Average time to close issues: 2 days
  • Average time to close pull requests: about 2 months
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.71
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Emiller88 (39)
  • edmundmiller (23)
  • Caffeinated-Code (3)
  • YoshikiHigashijima (2)
  • famosab (1)
  • bug1303 (1)
  • maxulysse (1)
  • andreagillespie (1)
  • jen-reeve (1)
  • dmitrymyl (1)
  • MathewBerg9 (1)
  • jianhong (1)
  • SR-46 (1)
  • dshechter (1)
Pull Request Authors
  • edmundmiller (41)
  • Emiller88 (36)
  • nf-core-bot (35)
  • sruthipsuresh (1)
  • ignaciot (1)
  • KevinMenden (1)
  • apeltzer (1)
Top Labels
Issue Labels
enhancement (30) bug (17) high-priority (1) documentation (1)
Pull Request Labels
bug (6)

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 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
  • github/super-linter v4 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/bbmap/pileup/meta.yml cpan
modules/nf-core/bedtools/genomecov/meta.yml cpan
modules/nf-core/bedtools/intersect/meta.yml cpan
modules/nf-core/bedtools/merge/meta.yml cpan
modules/nf-core/bedtools/sort/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/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/custom/getchromsizes/meta.yml cpan
modules/nf-core/deeptools/bamcoverage/meta.yml cpan
modules/nf-core/dragmap/align/meta.yml cpan
modules/nf-core/dragmap/hashtable/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gffread/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/homer/findpeaks/meta.yml cpan
modules/nf-core/homer/maketagdirectory/meta.yml cpan
modules/nf-core/homer/makeucscfile/meta.yml cpan
modules/nf-core/homer/pos2bed/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/pints/caller/meta.yml cpan
modules/nf-core/preseq/ccurve/meta.yml cpan
modules/nf-core/preseq/lcextrap/meta.yml cpan
modules/nf-core/rseqc/inferexperiment/meta.yml cpan
modules/nf-core/rseqc/readdistribution/meta.yml cpan
modules/nf-core/rseqc/readduplication/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/flagstat/meta.yml cpan
modules/nf-core/samtools/idxstats/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/stats/meta.yml cpan
modules/nf-core/subread/featurecounts/meta.yml cpan
modules/nf-core/umitools/dedup/meta.yml cpan
modules/nf-core/untar/meta.yml cpan
subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml cpan
subworkflows/nf-core/bam_sort_stats_samtools/meta.yml cpan
subworkflows/nf-core/bam_stats_samtools/meta.yml cpan
subworkflows/nf-core/homer/groseq/meta.yml cpan
pyproject.toml pypi