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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Assembly

Assemble transcripts with multiple tools.

Workflow	Tools	Input
long-read-rna	isonform, isonform-clustered, rattle, rattle-clustered, rnabloom2, rnabloom2-clustered, stringtie3	FASTQ + cluster TSV + BAM + GTF
short-read-rna	spades, trinity, bookend	paired-end FASTQ + BAM + FASTA

Haplotagging

Phase and haplotag reads with multiple tools.

Workflow	Tools	Input
long-read-dna	hapcut2-whatshap, hiphase, longphase, margin, whatshap	long-read DNA FASTQ
long-read-rna	flair3-longshot, longcallr	long-read RNA FASTQ
short-read-dna	hapcut2-whatshap, whatshap	short-read DNA FASTQ

HLA Typing

Type HLA alleles with multiple tools.

Workflow	Tools	Input
short-read-dna	hlaminer-sr-dna, optitype, spechla	paired-end FASTQ
short-read-rna	arcashla, hlaminer-sr-rna, hlaprofiler, seq2hla, optitype	BAM + paired-end FASTQ
long-read-dna	fufihla, hlaminer-lr-dna, spechla-lr-dna, specimmune	long-read FASTQ
long-read-rna	hlaminer-lr-rna, specimmune	long-read FASTQ

Isoform Characterization

Characterize transcript isoforms with multiple tools.

Workflow	Tools	Input
long-read	espresso, flair3, isoquant, isotools, lraa, mandalorion, sqanti3, talon	BAM + FASTQ + FASTA + GTF
short-read	rmats	BAM

Quantification

Quantify transcript expression with multiple tools.

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

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
long-read rna	clair3rna, de-souza, longgf, pbfusion	BAM + FASTQ