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omnifluss

Computational workflow for virus genome reconstruction

https://github.com/rki-mf1/omnifluss

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
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary

Keywords

genome-reconstruction nextflow nf-core virus
Last synced: 7 months ago · JSON representation ·

Repository

Computational workflow for virus genome reconstruction

Basic Info
Statistics
  • Stars: 8
  • Watchers: 1
  • Forks: 0
  • Open Issues: 21
  • Releases: 0
Topics
genome-reconstruction nextflow nf-core virus
Created about 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Citation

README.md

GitHub Release Static Badge GitHub Actions Workflow Status GitHub commit activity

rki-mf1/omnifluss

Introduction

rki-mf1/omnifluss is a bioinformatics pipeline for the reconstruction of virus genomes.

Omnifluss takes raw sequencing data and performs operations such as quality filtering, primer clipping, taxanomic classification, alignment, variant calling, consensus assembly, and optionally reference selection. The specific algorithms and software selected for these operations primarily depend on two parameters: virus type and sequencing technology. Beside these two parameters many settings and subroutines can be finetuned. After a successful run omnifluss returns a consensus sequence, intermediate files, and an HTML report that includes statistics of the individual operations.

Usage

Please visit our omnifluss website for our full documentation.

TL;DR (setup environment) You need Nextflow and at least one package manager (conda) or container engine (singularity, docker) available. You can install Nextflow via conda: ```bash conda create -n omnifluss -c bioconda -c conda-forge nextflow==25.04.3 conda activate omnifluss ```
TL;DR (run) ```bash nextflow run rki-mf1/omnifluss \ -profile \ --input samplesheet.csv \ --outdir ```

Credits

rki-mf1/omnifluss was originally written by the RKI MF1 Viroinf team.

Funding

This project was supported by co-funding from the European Union’s EU4Health programme under project no. 101113012 (IMS-HERA2).

Citations

<WIP>

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

Owner

  • Name: RKI MF1 Bioinformatics
  • Login: rki-mf1
  • Kind: organization
  • Location: Germany

Bioinformatics code of MF1

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Omnifluss
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - name: >-
      Viroinformatics, Genome Competence Centre (MF1),
      Robert Koch Institute
    address: Nordufer 20
    city: Berlin
    country: DE
    post-code: '13353'
    website: 'https://www.rki.de/EN/Home/homepage_node.html'
  - given-names: Marie
    family-names: Lataretu
    affiliation: Robert Koch Institute (RKI)
    orcid: 'https://orcid.org/0000-0002-3637-5870'
  - given-names: Dimitri
    family-names: Ternovoj
    affiliation: Robert Koch Institute (RKI)
  - given-names: Thomas
    family-names: Krannich
    affiliation: Robert Koch Institute (RKI)
    orcid: 'https://orcid.org/0000-0002-5525-1849'
repository-code: 'https://github.com/rki-mf1/omnifluss'
license: MIT

GitHub Events

Total
  • Create event: 26
  • Issues event: 23
  • Release event: 1
  • Watch event: 6
  • Delete event: 25
  • Issue comment event: 44
  • Push event: 134
  • Public event: 1
  • Pull request review event: 69
  • Pull request review comment event: 48
  • Pull request event: 58
Last Year
  • Create event: 26
  • Issues event: 23
  • Release event: 1
  • Watch event: 6
  • Delete event: 25
  • Issue comment event: 44
  • Push event: 134
  • Public event: 1
  • Pull request review event: 69
  • Pull request review comment event: 48
  • Pull request event: 58

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 18
  • Total pull requests: 34
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.83
  • Average comments per pull request: 0.5
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 34
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.83
  • Average comments per pull request: 0.5
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Krannich479 (14)
  • DimitriTernovoj (2)
  • MarieLataretu (2)
Pull Request Authors
  • DimitriTernovoj (14)
  • Krannich479 (12)
  • MarieLataretu (8)
Top Labels
Issue Labels
INV (8) enhancement (6) nf-test (3) bug (2) question (2)
Pull Request Labels
enhancement (5) nf-test (5) INV (3) documentation (3) bug (2) nf-core (1) nf-core hackathon 03/2025 (1)

Dependencies

modules/local/inv_create_consensus_mask_bedtools/meta.yml cpan
modules/local/inv_get_deletions_pyvcf/meta.yml cpan
modules/local/inv_process_reference_biopython/meta.yml cpan
modules/local/inv_reference_selection_grep/meta.yml cpan
modules/local/inv_rescue_variants_python/meta.yml cpan
modules/local/inv_set_gt_bcftools/meta.yml cpan
modules/nf-core/bcftools/consensus/meta.yml cpan
modules/nf-core/bcftools/filter/meta.yml cpan
modules/nf-core/bcftools/index/meta.yml cpan
modules/nf-core/bcftools/norm/meta.yml cpan
modules/nf-core/bwa/index/meta.yml cpan
modules/nf-core/bwa/mem/meta.yml cpan
modules/nf-core/cat/cat/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/kraken2/kraken2/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/seqkit/grep/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
subworkflows/local/bam_call_variant_all/meta.yml cpan
subworkflows/local/bam_special_variants_case_all/meta.yml cpan
subworkflows/local/fasta_process_reference_all/meta.yml cpan
subworkflows/local/fasta_reference_selection_all/meta.yml cpan
subworkflows/local/fastq_map_all/meta.yml cpan
subworkflows/local/fastq_qc_trimming_all/meta.yml cpan
subworkflows/local/fastq_taxonomic_filtering_all/meta.yml cpan
subworkflows/local/vcf_call_consensus_all/meta.yml cpan
subworkflows/nf-core/bam_markduplicates_picard/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/fastq_align_bwa/meta.yml cpan
subworkflows/nf-core/fastq_extract_kraken_krakentools/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/krakentools/extractkrakenreads/meta.yml cpan
modules/nf-core/lofreq/callparallel/meta.yml cpan
modules/nf-core/lofreq/filter/meta.yml cpan
modules/nf-core/lofreq/indelqual/meta.yml cpan
modules/nf-core/lofreq/viterbi/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/picard/markduplicates/meta.yml cpan
modules/nf-core/samtools/depth/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/local/inv_create_consensus_mask_bedtools/environment.yml conda
  • bedtools 2.31.1.*
modules/local/inv_get_deletions_pyvcf/environment.yml conda
  • pyvcf 0.6.8
modules/local/inv_process_reference_biopython/environment.yml conda
  • biopython 1.73
modules/local/inv_referenceSelection_kma/environment.yml conda
  • kma 1.4.15
modules/local/inv_reference_selection_grep/environment.yml conda
  • gnu-coreutils 9.5
  • grep 3.4
modules/local/inv_rescue_variants_python/environment.yml conda
  • python 3.12.*
modules/local/inv_set_gt_bcftools/environment.yml conda
  • bcftools 1.20.*
modules/nf-core/bcftools/consensus/environment.yml conda
  • bcftools 1.20.*
modules/nf-core/bcftools/filter/environment.yml conda
  • bcftools 1.20.*
modules/nf-core/bcftools/index/environment.yml conda
  • bcftools 1.20.*
modules/nf-core/bcftools/norm/environment.yml conda
  • bcftools 1.20.*
modules/nf-core/bwa/index/environment.yml conda
  • bwa 0.7.18.*
modules/nf-core/bwa/mem/environment.yml conda
  • bwa 0.7.18.*
  • htslib 1.20.0.*
  • samtools 1.20.*
modules/nf-core/cat/cat/environment.yml conda
  • pigz 2.3.4.*
modules/nf-core/fastp/environment.yml conda
  • fastp 0.23.4.*
modules/nf-core/fastqc/environment.yml conda
  • fastqc 0.12.1.*
modules/nf-core/gunzip/environment.yml conda
  • grep 3.11.*
  • sed 4.8.*
  • tar 1.34.*
modules/nf-core/kraken2/kraken2/environment.yml conda
  • coreutils 9.4.*
  • kraken2 2.1.3.*
  • pigz 2.8.*
modules/nf-core/krakentools/extractkrakenreads/environment.yml conda
  • krakentools 1.2.*
modules/nf-core/lofreq/callparallel/environment.yml conda
  • lofreq 2.1.5.*
modules/nf-core/lofreq/filter/environment.yml conda
  • lofreq 2.1.5.*
modules/nf-core/lofreq/indelqual/environment.yml conda
  • lofreq 2.1.5.*
modules/nf-core/lofreq/viterbi/environment.yml conda
  • lofreq 2.1.5.*
  • samtools 1.17.*
modules/nf-core/multiqc/environment.yml conda
  • multiqc 1.22.2.*
modules/nf-core/picard/markduplicates/environment.yml conda
  • picard 3.2.0.*
modules/nf-core/samtools/depth/environment.yml conda
  • htslib 1.21.*
  • samtools 1.21.*
modules/nf-core/samtools/faidx/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/flagstat/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/idxstats/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/index/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/sort/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/samtools/stats/environment.yml conda
  • htslib 1.20.*
  • samtools 1.20.*
modules/nf-core/seqkit/grep/environment.yml conda
  • seqkit 2.8.1.*
modules/nf-core/tabix/tabix/environment.yml conda
  • htslib 1.19.1.*
  • tabix 1.11.*