Workflows

Multi-tool pipelines

Each workflow orchestrates multiple subworkflows into an end-to-end pipeline. Supply a params.yaml file and run.

nexus run --nf-workflow <workflow>.nf -params-file params.yaml

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Variant Calling

Run multiple variant callers in parallel on the same samples.

Workflow	Tools	Input
long-read germline	clair3, cutesv, deepvariant, delly2, dysgu, hificnv, longshot, nanocaller, nanovar, pbsv, sniffles2, svim	single-sample BAM
long-read somatic	clairs, deepsomatic, delly2, dysgu, nanomonsv, savana, severus, svisionpro	tumor/normal BAM
short-read germline	clair3, deepvariant, delly2, dysgu, gridss2, haplotypecaller, lumpy, manta, octopus, pindel, strelka2	single-sample BAM
short-read somatic	clairs, deepsomatic, delly2, dysgu, gridss2, lumpy, manta, mutect2, octopus, sequenza, strelka2, svaba	tumor/normal BAM

Quantification

Quantify transcript expression with multiple tools.

Workflow	Tools	Input
long-read	bambu, kallisto, liqa, oarfish, transigner	BAM + FASTQ
short-read	kallisto, salmon	paired-end FASTQ

Isoform Characterization

Characterize transcript isoforms with multiple tools.

Workflow	Tools	Input
long-read	espresso, flair, isoquant, isotools, mandalorion, sqanti3, talon	BAM + FASTQ + FASTA + GTF
short-read	rmats	BAM

HLA Typing

Type HLA alleles with multiple tools.

Workflow	Tools	Input
short-read	arcashla, hlaprofiler, seq2hla	BAM + paired-end FASTQ