Subworkflows
Single-tool workflows
Each subworkflow wraps one bioinformatics tool into a ready-to-run Nextflow workflow. Pick a tool, provide a samples TSV and reference files, and go.
nexus run --nf-workflow <subworkflow>.nf \
-c nextflow.config -w work/ \
--samples_tsv_file samples.tsv \
--output_dir results/ \
[tool-specific parameters]| Tool | Description |
|---|---|
| blastp | protein sequence alignment |
| bwamem2 | short-read DNA alignment with ABRA2 realignment |
| diamond-blastp | fast protein alignment |
| minimap2 | long-read alignment |
| minimap2-dynamic | long-read alignment with dynamic reference |
| star | short-read RNA alignment |
| ultra | long-read RNA alignment |
| Tool | Description |
|---|---|
| mhcflurry2 | MHC-I binding prediction |
| mhcflurry2-scan | MHC-I binding scan mode |
| netmhcpan4 | MHC-I binding prediction |
| Tool | Description |
|---|---|
| hifiasm | de novo assembly from HiFi reads |
| rattle | long-read RNA isoform clustering |
| rnabloom2 | long-read RNA assembly |
| stringtie2 | transcript assembly |
| stringtie3 | long-read transcript assembly |
| Tool | Description |
|---|---|
| flair-longshot | long-read RNA variant phasing + haplotagging |
| hapcut2-whatshap | short-read variant phasing + haplotagging |
| hiphase | PacBio long-read phasing + haplotagging (SNV + SV) |
| longcallr | long-read RNA variant calling, phasing, haplotagging |
| longphase | long-read variant phasing + haplotagging |
| longshot | long-read SNV phasing + haplotagging |
| margin | long-read variant phasing + haplotagging |
| whatshap | read-backed phasing + haplotagging |
| Tool | Description |
|---|---|
| arcashla | HLA typing from RNA-seq BAM |
| hlaminer-lr-rna | long-read RNA HLA typing (minimap2 + HLAminer) |
| hlaprofiler | HLA typing from FASTQ |
| seq2hla | HLA typing from FASTQ |
| specimmune | long-read HLA / KIR / CYP / IG_TR typing |
| Tool | Description |
|---|---|
| espresso | isoform detection from long reads |
| flair | isoform detection from long reads |
| isoquant | transcript quantification and discovery |
| isoseq | PacBio Iso-Seq clustering |
| isotools | long-read isoform analysis |
| mandalorion | isoform detection from long reads |
| rmats | differential alternative splicing |
| sqanti3-fasta | isoform QC (FASTA mode) |
| sqanti3-gtf | isoform QC (GTF mode) |
| talon | long-read transcriptome annotation |
| Tool | Description |
|---|---|
| exacto | long-read mutant proteoform prediction pipeline |
| mopepgen-gencode | mutant peptide prediction |
| Tool | Description |
|---|---|
| bambu | long-read transcript quantification |
| kallisto-lr | long-read pseudoalignment quantification |
| kallisto-pe | paired-end pseudoalignment quantification |
| liqa | long-read isoform quantification |
| oarfish | long-read transcript quantification |
| salmon-fastq | paired-end transcript quantification |
| transigner | long-read transcript quantification |
| Tool | Description |
|---|---|
| ratatosk | hybrid error correction |
| Tool | Description |
|---|---|
| art-illumina-pe | Illumina paired-end simulation |
| beers2 | RNA-seq Illumina paired-end simulation |
| nanosim-genome | Nanopore read simulation |
| neat | Illumina read simulation |
| pbsim3-dna | PacBio DNA read simulation |
| pbsim3-rna | PacBio RNA read simulation |
| Tool | Description |
|---|---|
| cutadapt | adapter and polyA trimming |
| fastq2unalignedbam | FASTQ to unaligned BAM |
| fastqc | read quality control |
| filter-rnabloom2-transcripts | filter assembled transcripts |
| pbccs | PacBio circular consensus |
| sequencing-coverage | sequencing coverage statistics |
| Tool | Description |
|---|---|
| vep | variant effect prediction |
| vep-custom | VEP with custom annotation |
| Tool | Description |
|---|---|
| arriba | RNA fusion detection |
| circexplorer2 | circular RNA detection |
| clair3 | germline SNV/indel calling (long-read) |
| clair3rna | RNA variant calling (long-read) |
| clairs | somatic SNV/indel calling (long-read) |
| colorsv | somatic SV calling from GFA |
| cutesv | germline SV calling (long-read) |
| de-souza | RNA variant calling pipeline |
| deepsomatic | somatic SNV/indel calling (long-read) |
| deepvariant | germline SNV/indel calling |
| delly2-lr-germline | germline SV calling (long-read) |
| delly2-lr-somatic | somatic SV calling (long-read) |
| delly2-sr-germline | germline SV calling (short-read) |
| delly2-sr-somatic | somatic SV calling (short-read) |
| dysgu-germline | germline SV calling |
| dysgu-somatic | somatic SV calling |
| gridss2-germline | germline SV calling (short-read) |
| gridss2-somatic | somatic SV calling (short-read) |
| haplotypecaller | germline SNV/indel calling (short-read) |
| hificnv | copy number calling (HiFi) |
| himut | somatic SNV calling (long-read) |
| longgf | gene fusion detection (long-read) |
| longshot | germline SNV calling (long-read) |
| lumpy-germline | germline SV calling (short-read) |
| lumpy-somatic | somatic SV calling (short-read) |
| manta-germline | germline SV calling (short-read) |
| manta-somatic | somatic SV calling (short-read) |
| mutect2 | somatic SNV/indel calling (short-read) |
| nanocaller | germline SNV/indel calling (long-read) |
| nanomonsv | somatic SV calling (long-read) |
| nanovar | germline SV calling (long-read) |
| octopus-germline | germline variant calling (short-read) |
| octopus-somatic | somatic variant calling (short-read) |
| pbfusion | gene fusion detection (HiFi) |
| pbsv | germline SV calling (HiFi) |
| pindel | indel and SV detection (short-read) |
| reditools2 | RNA editing detection |
| savana | somatic SV calling (long-read) |
| sequenza | copy number and cellularity estimation |
| severus | somatic SV calling (long-read) |
| sniffles2 | germline SV calling (long-read) |
| starfusion | RNA fusion detection |
| strelka2-germline | germline SNV/indel calling (short-read) |
| strelka2-somatic | somatic SNV/indel calling (short-read) |
| svaba | somatic SV and indel calling (short-read) |
| svim | germline SV calling (long-read) |
| svisionpro | somatic SV calling (long-read) |