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smallvariants

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

https://github.com/nf-cmgg/smallvariants

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary

Keywords

annotation cram genotyping germline germline-variant-calling ngs ngs-pipeline short-reads
Last synced: 6 months ago · JSON representation ·

Repository

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Basic Info
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 3
  • Open Issues: 16
  • Releases: 26
Topics
annotation cram genotyping germline germline-variant-calling ngs ngs-pipeline short-reads
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

nf-cmgg/smallvariants

GitHub Actions CI Status GitHub Actions Linting Status nf-test

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

Introduction

nf-cmgg/smallvariants is a nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data.

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!

Please have a look at the documentation on how to run the pipeline.

Owner

  • Name: Center For Medical Genetics Ghent - Nextflow workflows
  • Login: nf-cmgg
  • Kind: organization
  • Email: ict@cmgg.be
  • Location: Belgium

Center For Medical Genetics Ghent - Ghent University Hospital - Nextflow workflows

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
authors:
    - family-names: Ewels
      given-names: Philip
    - family-names: Peltzer
      given-names: Alexander
    - family-names: Fillinger
      given-names: Sven
    - family-names: Patel
      given-names: Harshil
    - family-names: Alneberg
      given-names: Johannes
    - family-names: Wilm
      given-names: Andreas
    - family-names: Garcia
      given-names: Maxime Ulysse
    - family-names: Di Tommaso
      given-names: Paolo
    - family-names: Nahnsen
      given-names: Sven
title: "The nf-core framework for community-curated bioinformatics pipelines."
version: 2.4.1
doi: 10.1038/s41587-020-0439-x
date-released: 2022-05-16
url: https://github.com/nf-core/tools
prefered-citation:
    type: article
    authors:
        - family-names: Ewels
          given-names: Philip
        - family-names: Peltzer
          given-names: Alexander
        - family-names: Fillinger
          given-names: Sven
        - family-names: Patel
          given-names: Harshil
        - family-names: Alneberg
          given-names: Johannes
        - family-names: Wilm
          given-names: Andreas
        - family-names: Garcia
          given-names: Maxime Ulysse
        - family-names: Di Tommaso
          given-names: Paolo
        - family-names: Nahnsen
          given-names: Sven
    doi: 10.1038/s41587-020-0439-x
    journal: nature biotechnology
    start: 276
    end: 278
    title: "The nf-core framework for community-curated bioinformatics pipelines."
    issue: 3
    volume: 38
    year: 2020
    url: https://dx.doi.org/10.1038/s41587-020-0439-x

GitHub Events

Total
  • Create event: 12
  • Release event: 2
  • Issues event: 3
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 10
  • Push event: 51
  • Pull request review comment event: 6
  • Pull request review event: 16
  • Pull request event: 24
  • Fork event: 2
Last Year
  • Create event: 12
  • Release event: 2
  • Issues event: 3
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 10
  • Push event: 51
  • Pull request review comment event: 6
  • Pull request review event: 16
  • Pull request event: 24
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 14
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.07
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 14
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Issue authors: 2
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.07
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nvnieuwk (1)
  • matthdsm (1)
Pull Request Authors
  • nvnieuwk (7)
  • matthdsm (5)
  • ThomasSte01 (1)
  • Tuur-ds (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Dependencies

.github/workflows/linting.yml actions
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modules/nf-core/bcftools/pluginscatter/meta.yml cpan
modules/nf-core/bcftools/query/meta.yml cpan
modules/nf-core/bcftools/reheader/meta.yml cpan
modules/nf-core/bcftools/sort/meta.yml cpan
modules/nf-core/bcftools/stats/meta.yml cpan
modules/nf-core/bedtools/intersect/meta.yml cpan
modules/nf-core/bedtools/merge/meta.yml cpan
modules/nf-core/bedtools/split/meta.yml cpan
modules/nf-core/ensemblvep/vep/meta.yml cpan
modules/nf-core/gatk4/calibratedragstrmodel/meta.yml cpan
modules/nf-core/gatk4/composestrtablefile/meta.yml cpan
modules/nf-core/gatk4/createsequencedictionary/meta.yml cpan
modules/nf-core/gatk4/genomicsdbimport/meta.yml cpan
modules/nf-core/gatk4/genotypegvcfs/meta.yml cpan
modules/nf-core/gatk4/haplotypecaller/meta.yml cpan
modules/nf-core/mosdepth/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/rtgtools/format/meta.yml cpan
modules/nf-core/rtgtools/pedfilter/meta.yml cpan
modules/nf-core/rtgtools/rocplot/meta.yml cpan
modules/nf-core/rtgtools/vcfeval/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/merge/meta.yml cpan
modules/nf-core/somalier/extract/meta.yml cpan
modules/nf-core/somalier/relate/meta.yml cpan
modules/nf-core/tabix/bgzip/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
modules/nf-core/untar/meta.yml cpan
modules/nf-core/vcf2db/meta.yml cpan
modules/nf-core/vcfanno/meta.yml cpan
assets/Dockerfile docker
  • mambaorg/micromamba 1.4-focal build
modules/nf-core/bcftools/norm/meta.yml cpan
modules/nf-core/ensemblvep/download/meta.yml cpan
modules/nf-core/gawk/meta.yml cpan
modules/nf-core/samtools/convert/meta.yml cpan
modules/nf-core/tabix/bgziptabix/meta.yml cpan
modules/nf-core/vardictjava/meta.yml cpan
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  • nf-core/setup-nextflow b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 composite
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
.github/workflows/build-docs.yml actions
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modules/nf-core/elprep/fastatoelfasta/meta.yml cpan
modules/nf-core/elprep/filter/meta.yml cpan
subworkflows/local/vcf_annotate_ensemblvep/meta.yml cpan
subworkflows/nf-core/utils_nfschema_plugin/meta.yml cpan
modules/nf-core/elprep/fastatoelfasta/environment.yml conda
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modules/nf-core/elprep/filter/environment.yml conda
  • elprep 5.1.3.*
modules/nf-core/ensemblvep/vep/environment.yml conda
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modules/nf-core/bcftools/pluginscatter/environment.yml pypi
modules/nf-core/bcftools/query/environment.yml pypi
modules/nf-core/bcftools/reheader/environment.yml pypi
modules/nf-core/bcftools/sort/environment.yml pypi
modules/nf-core/bcftools/stats/environment.yml pypi
modules/nf-core/bedtools/intersect/environment.yml pypi
modules/nf-core/bedtools/merge/environment.yml pypi
modules/nf-core/bedtools/split/environment.yml pypi
modules/nf-core/ensemblvep/download/environment.yml pypi
modules/nf-core/gatk4/calibratedragstrmodel/environment.yml pypi
modules/nf-core/gatk4/composestrtablefile/environment.yml pypi
modules/nf-core/gatk4/createsequencedictionary/environment.yml pypi
modules/nf-core/gatk4/genomicsdbimport/environment.yml pypi
modules/nf-core/gatk4/genotypegvcfs/environment.yml pypi
modules/nf-core/gatk4/haplotypecaller/environment.yml pypi
modules/nf-core/gawk/environment.yml pypi
modules/nf-core/mosdepth/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/rtgtools/format/environment.yml pypi
modules/nf-core/rtgtools/pedfilter/environment.yml pypi
modules/nf-core/rtgtools/rocplot/environment.yml pypi
modules/nf-core/rtgtools/vcfeval/environment.yml pypi
modules/nf-core/samtools/convert/environment.yml pypi
modules/nf-core/samtools/faidx/environment.yml pypi
modules/nf-core/samtools/index/environment.yml pypi
modules/nf-core/samtools/merge/environment.yml pypi
modules/nf-core/somalier/extract/environment.yml pypi
modules/nf-core/somalier/relate/environment.yml pypi
modules/nf-core/tabix/bgzip/environment.yml pypi
modules/nf-core/tabix/bgziptabix/environment.yml pypi
modules/nf-core/tabix/tabix/environment.yml pypi
modules/nf-core/untar/environment.yml pypi
modules/nf-core/vardictjava/environment.yml pypi
modules/nf-core/vcf2db/environment.yml pypi
modules/nf-core/vcfanno/environment.yml pypi