Data

Tools

Indexes

Applications

Experiments

Open Source Science

ear

ERGA Assembly Report pipeline

https://github.com/sanger-tol/ear

Science Score: 75.0%

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 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization sanger-tol has institutional domain (www.sanger.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords

genomics nextflow pipeline reporting-tool workflow
Last synced: 6 months ago · JSON representation ·

Repository

ERGA Assembly Report pipeline

Basic Info
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 3
  • Releases: 4
Topics
genomics nextflow pipeline reporting-tool workflow
Created over 1 year ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

sanger-tol/ear

GitHub Actions CI Status GitHub Actions Linting StatusDOI nf-test

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

Introduction

sanger-tol/ear is a bioinformatics pipeline that generates the data files required for the the generation of ERGA Assembly Reports. Sanger-tol/ear nests two other sanger-tol pipelines (blobtoolkit and curationpretext).

  1. Read the input yaml file (YAML_INPUT)
  2. Run GFASTATS (GFASTARS)
  3. Run MERQURYFK_MERQURYFK (MERQURYFK)
  4. Run MAIN_MAPPING, longread single-end/paired-end mapping
  5. Run GENERATESAMPLESHEET, generate a csv file required for SANGERTOL_BTK.
  6. Run SANGERTOLBTK, also known as SANGER-TOL/BLOBTOOLKIT a subpipline for SANGER-TOL/EAR
  7. Run SANGERTOLCPRETEXT, also known as SANGER-TOL/CURATIONPRETEXT a subpipeline for SANGER-TOL/EAR.

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.

The sanger-tol/ear pipeline requires a number of databases in place in order to run the blobtoolkit pipeline. These include:

  • A blast nt database
  • A Diamond blast uniprot database
  • A Diamond blast nr database
  • An NCBI taxdump
  • An NCBI rankedlineage.dmp

Next, a yaml file containing the following should then be completed:

```yaml

General Vales for all subpiplines and modules

assemblyid: referencehap1: referencehap2: referencehaplotigs:

If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore it and the pipeline will create it.

mapped_bam:

merquryfk: fastkhist: fastkktab:

Used by both subpipelines

longread: type: dir: curationpretext: aligner: telomeremotif: hicdir: btk: taxid: 1464561 lineages: < CSV LIST OF DATABASES TO USE: "insectaodb10,dipteraodb10"> gcaaccession: GCA0001

ntdatabase: ntdatabaseprefix: diamonduniprotdatabasepath: diamondnrdatabasepath: ncbitaxonomypath: ncbirankedlineage_path: config: ```

Now, you can run the pipeline using:

bash nextflow run sanger-tol/ear -profile <singularity,docker> \\ --input assets/idCulLati1.yaml \\ --mapped TRUE \\ # OPTIONAL --steps ["", "btk", "cpretext", "merquryfk"] # OPTIONAL CSV LIST OF STEPS TO EXCLUDE FROM EXECUTION --outdir test

[!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.

Credits

sanger-tol/ear was originally written by DLBPointon.

Contributions and Support

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

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: Tree of Life programme
  • Login: sanger-tol
  • Kind: organization
  • Location: United Kingdom

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology

Citation (CITATIONS.md) 

# sanger-tol/ear: 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

- [GFastar/GFastats](https://www.biorxiv.org/content/10.1101/2022.03.24.485682v1)

  > Formenti, G., Abueg, L., Brajuka, N., Gallardo, C., Giani, A., Fedrigo, O., Jarvis, ED. (2022). Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. bioRxiv. doi: https://doi.org/10.1101/2022.03.24.485682

- [Merqury_FK](https://github.com/thegenemyers/MERQURY.FK)

  > Myers, G., Rhie, A. (2024). MerquryFK & KatFK. [online]. https://github.com/thegenemyers/MERQURY.FK. (Accessed on 20 September 2024).

- [Minimap2](https://pubmed.ncbi.nlm.nih.gov/34623391/)

  > Li, H. 2021. ‘New strategies to improve MINIMAP2 alignment accuracy’, Bioinformatics, 37(23), pp. 4572–4574. doi:10.1093/bioinformatics/btab705.

- [Samtools](https://pubmed.ncbi.nlm.nih.gov/33590861/)

  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.

- [sanger-tol/blobtoolkit](https://zenodo.org/records/13758882)

  > Muffato, M., Butt, Z., Challis, R., Kumar, S., Qi, G., Ramos Díaz, A., Surana, P., & Yates, B. (2024). sanger-tol/blobtoolkit: v0.6.0 – Bellsprout (0.6.0). Zenodo. https://doi.org/10.5281/zenodo.13758882

- [sanger-tol/curationpretext](https://zenodo.org/records/13758882)

  > Pointon, DLB. (2024). sanger-tol/curationpretext: v1.0.0 (UNSC Cradle). [online]. https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0. (Accessed on 20 September 2024).

## Software packaging/containerisation tools

- [Conda](https://conda.org/)

  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda

- [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: 15
  • Issues event: 7
  • Release event: 2
  • Delete event: 9
  • Member event: 1
  • Issue comment event: 25
  • Push event: 74
  • Pull request review event: 2
  • Pull request event: 32
Last Year
  • Create event: 15
  • Issues event: 7
  • Release event: 2
  • Delete event: 9
  • Member event: 1
  • Issue comment event: 25
  • Push event: 74
  • Pull request review event: 2
  • Pull request event: 32

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 15
  • Average time to close issues: 3 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.75
  • Average comments per pull request: 1.4
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 15
  • Average time to close issues: 3 months
  • Average time to close pull requests: 6 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.75
  • Average comments per pull request: 1.4
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • DLBPointon (6)
Pull Request Authors
  • DLBPointon (22)
Top Labels
Issue Labels
bug (3) enhancement (2)
Pull Request Labels
enhancement (3) documentation (1)

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
.github/workflows/ci.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
.github/workflows/linting.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • actions/upload-artifact 65462800fd760344b1a7b4382951275a0abb4808 composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact 09f2f74827fd3a8607589e5ad7f9398816f540fe composite
  • marocchino/sticky-pull-request-comment 331f8f5b4215f0445d3c07b4967662a32a2d3e31 composite
.github/workflows/release-announcements.yml actions
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action 80dbe0a7697de18c15ad22f4619919ceb5ccf597 composite
modules/nf-core/busco/busco/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gfastats/meta.yml cpan
modules/nf-core/merquryfk/merquryfk/meta.yml cpan
modules/nf-core/minimap2/align/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/merge/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
modules/nf-core/busco/busco/environment.yml conda
  • busco 5.7.1.*
modules/nf-core/fastqc/environment.yml conda
  • fastqc 0.12.1.*
modules/nf-core/gfastats/environment.yml conda
  • gfastats 1.3.6.*
modules/nf-core/merquryfk/merquryfk/environment.yml conda
modules/nf-core/minimap2/align/environment.yml conda
  • htslib 1.20.*
  • minimap2 2.28.*
  • samtools 1.20.*
modules/nf-core/multiqc/environment.yml conda
  • multiqc 1.21.*
modules/nf-core/samtools/merge/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/sort/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*