Introduction

DelMoro is a Nextflow pipeline for genome/exome variant detection across species specifically used in Human clinical genomics, offering two modality executions. As it can be executed as a complete end-to-end workflow or as a collection of independent analysis modules : (I) stepmode for modular execution of 9 subworkflows and (II) fullmode for automated end-to-end analysis.

The complete list of software used by DelMoro, together with the corresponding citations, is provided in TOOLS.md.

Usage

Warning

The pipeline is compatible with Nextflow v26.x or earlier.

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Detailed documentation, including installation instructions, pipeline configuration, input requirements, and execution examples, is available at: documentation link

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Note

Please make sure to check help menu with --help before running the workflow on actual data.

 nextflow run main.nf --help

Usage   : nextflow run main.nf <modality> [--exec <module>] <params>

Modality: - --fullmode  : Executing   full   mode from fastq until vaiant calling.
          - --stepmode  : Executing   different   modules   in   standalone  mode.

Executing fullmode :

nextflow run main.nf  
    --fullmode
    --input  
    --reference   | [--igenome ]   
    [--aligner bwamem2]  
    [--bqsr]  
    [--knownsite1 ,--knownsite2 |--ivcf1 ,--ivcf2 ]
    [--caller deepvariant ]
    [--mode cohort]  

Executing stepmode :

nextflow run main.nf  
    --stepmode
    --exec <module>   

Module  : - rawqc       : Check           quality      of     raw           reads. 
          - trim        : Remove low-quality bp and adapters & checks its quality.
          - refidx      : Index   the    reference   genome    for      alignment.
          - align       : Align     reads      to     the     reference    genome.
          - bqsr        : Base          Quality         Score       recalibration.
          - callvar     : Detect          Variants   from      aligned      reads.
          - annotate    : annotate                  vfc                      file.
          - reporting   : Auto          Generate   PDF    of      vcf     reports.   
          - filter 	    : Filter  	vcfs  	     to      SNP      and      INDELS.                                                                                                                                      
          - help                                                                                                                                                                                                           
          - version 

Graphical User Interface

DelMoro graphical user interface (GUI) is available in the Releases section of this repository. To use it, download the executable GUI file.

Citations

If you use this pipeline in your research, please cite this GitHub repository.

Zemzem, F., H'mida, D., & Othman, H. (2026). DelMoro : A Nextflow Pipeline for Variant Calling and Streamlined Reporting in Clinical Genomics (Version 1.0.0) [Computer software]. https://github.com/othmanResearch/DelMoro

@software{Zemzem_DelMoro_A_2026,
author = {Zemzem, Firas and H'mida, Dorra and Othman, houcemeddine},
month = aug,
title = {{DelMoro : A Nextflow Pipeline for Variant Calling and  Streamlined Reporting in Clinical Genomics}},
url = {https://github.com/othmanResearch/DelMoro},
version = {1.0.0},
year = {2026}
}

Licence