Nexus

NEXtflow's Ultimate Streamliner

Command-line interface (CLI) for running bioinformatics workflows written in nextflow.

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01. Installation

Download the latest stable release here

Make sure to have nextflow v24.10.0 and up:

conda create -n nexus python=3.10
conda activate nexus
conda install bioconda::nextflow==24.10.0
pip install nexus-<version>.tar.gz --verbose

02. Dependencies

• python (>=3.10)
• nextflow (>=24.10.0)

03. Usage

To view all available workflows

nexus avail

To run a workflow

nexus run [-h] [--nf-workflow NF_WORKFLOW] [workflow-specific parameters]

To view workflow-specific parameters

nexus run --nf-workflow [NF_WORKFLOW] --help

04. Example

Long-read whole-genome sequencing fastq.gz alignment to a reference genome.

I/O	Description
Input	fastq.gz file for each sample.
Ouptut	MD-tagged and sorted bam and bam.bai files for each sample.

nexus run --nf-workflow long_read_alignment_minimap2.nf \
    -c NEXTFLOW_CONFIG_FILE \
    -w WORK_DIR \
    --samples_tsv_file SAMPLES_TSV_FILE \
    --output_dir OUTPUT_DIR \
    --reference_genome_fasta_file REFERENCE_GENOME_FASTA_FILE \
    --reference_genome_fasta_fai_file REFERENCE_GENOME_FASTA_FAI_FILE \
    --params_minimap2 '"-ax map-hifi --cs --eqx -Y -L"'

NEXTFLOW_CONFIG_FILE can be downloaded from here.

SAMPLES_TSV_FILE is a tab-delimited file:

Header	Description
sample_id	Sample ID
fastq_file	Full path to fastq.gz file

For more on this particular workflow, check out here.

05. Documentation for Available Workflows

A list of links to documentation for all available workflows in the latest version is provided below:

Category	Workflow
Alignment	long_read_alignment_minimap2.nf
Alignment	long_read_rna_alignment_ultra.nf
Alignment	paired-end_read_dna_alignment_bwa-mem2.nf
Alignment	paired-end_read_rna_alignment_star.nf
Alignment	peptide_alignment_blastp.nf
Antigen presentation prediction	antigen_presentation_prediction_mhcflurry2.nf
Assembly	transcriptome_assembly_rnabloom2.nf
Assembly	transcriptome_assembly_stringtie2.nf
Haplotyping	long_read_dna_haplotyping_whatshap.nf
HLA typing	paired-end_read_rna_hla_typing_arcashla.nf
HLA typing	paired-end_read_rna_hla_typing_hlaprofiler.nf
HLA typing	paired-end_read_rna_hla_typing_seq2hla.nf
Novel isoform discovery	novel_isoform_discovery_flair.nf
Novel isoform discovery	novel_isoform_discovery_isoquant.nf
Novel isoform discovery	novel_isoform_discovery_isoseq.nf
Quantification (RNA)	long_read_rna_quantification_bambu.nf
Quantification (RNA)	long_read_rna_quantification_kallisto.nf
Quantification (RNA)	long_read_rna_quantification_liqa.nf
Quantification (RNA)	long_read_rna_quantification_oarfish.nf
Quantification (RNA)	long_read_rna_quantification_transigner.nf
Quantification (RNA)	paired-end_read_rna_quantification_salmon_mapping.nf
Quantification (RNA)	paired-end_read_rna_quantification_kallisto.nf
Read error correction	long_read_error_correction_ratatosk.nf
Utilities	fastq_to_unaligned_bam.nf
Utilities	fastqc.nf
Utilities	sequencing_coverage.nf
Variant calling (DNA)	long_read_dna_variant_calling_clairs.nf
Variant calling (DNA)	long_read_dna_variant_calling_cutesv.nf
Variant calling (DNA)	long_read_dna_variant_calling_deepvariant.nf
Variant calling (DNA)	long_read_dna_variant_calling_dysgu.nf
Variant calling (DNA)	long_read_dna_variant_calling_nanomonsv.nf
Variant calling (DNA)	long_read_dna_variant_calling_pbsv.nf
Variant calling (DNA)	long_read_dna_variant_calling_savana.nf
Variant calling (DNA)	long_read_dna_variant_calling_severus.nf
Variant calling (DNA)	long_read_dna_variant_calling_sniffles2.nf
Variant calling (DNA)	long_read_dna_variant_calling_svim.nf
Variant calling (DNA)	long_read_dna_variant_calling_svisionpro.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_delly2.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_dysgu.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_gridss.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_lumpy.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_manta.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_mutect2.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_sequenza.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_strelka2.nf
Variant calling (DNA)	paired-end_read_dna_variant_calling_svaba.nf
Variant calling (RNA)	long_read_rna_variant_calling_clair3rna.nf
Variant calling (RNA)	long_read_rna_variant_calling_de_souza.nf
Variant calling (RNA)	paired-end_read_rna_variant_calling_arriba.nf
Variant phasing (DNA)	long_read_dna_variant_phasing_hiphase.nf
Variant phasing (DNA)	long_read_dna_variant_phasing_whatshap.nf