nf-core Templates¶
Templates for nf-core pipelines. Each template configures a complete Depictio project (data collections, recipes, dashboards and cross-DC links) from a single depictio ingest command.
| Template | Pipeline | Versions |
|---|---|---|
| ampliseq | 16S / ITS / CO1 amplicon sequencing | 2.14.0, 2.16.0, 2.18.0 |
| viralrecon | Viral assembly and variant calling | 3.0.0 |
| variantbenchmarking | Variant caller benchmarking against truth sets | 1.4.0 |
| differentialabundance | DESeq2 differential expression | 2.0.0 |
| funcscan | Functional screening of assembled contigs | 4.0.0 |
| airrflow | B and T cell receptor repertoire (AIRR) | 5.1.0, 5.1.1, 5.1.2 |
| rnafusion | Gene-fusion detection from RNA-seq | 4.1.3 |
| rnaseq | Bulk RNA-seq quantification | 3.26.0 |
| taxprofiler | Metagenomic taxonomic profiling | 2.0.1 |
| chipseq | Transcription-factor / histone ChIP-seq | 2.1.0 |
| atacseq | Chromatin accessibility (ATAC-seq) | 2.1.2 |
| cutandrun | CUT&RUN / CUT&Tag chromatin profiling | 3.1, 3.2.2 |
| eager | Ancient DNA authentication and genotyping | 2.4.5 |
| hic | Chromosome conformation capture (Hi-C) | 2.0.0, 2.1.0 |
| mag | Metagenome assembly and binning | 5.5.0 |
| methylseq | Bisulfite and enzymatic methylation sequencing | 2.3.0 |
| nanoseq | Nanopore long-read sequencing | 3.0.0 |
| sarek | Germline and somatic variant calling | 3.10.0, 3.11.0 |
| scrnaseq | Single-cell RNA-seq preprocessing | 4.2.0 |
| riboseq | Ribosome profiling | 2.0.0 |
| smrnaseq | Small RNA sequencing | 2.4.1 |
| genomeassembler | De novo genome assembly | 2.0.0 |
| mhcquant | Immunopeptidomics | 3.2.0 |
| demultiplex | Sequencing run demultiplexing | 1.8.0 |
| rnasplice | Alternative splicing analysis | 1.0.4 |
| proteinfamilies | Protein family clustering and profile HMMs | 2.5.0 |
| proteinannotator | Protein domain and structure annotation | 1.1.0 |
| proteinfold | Protein structure prediction | 2.1.0 |
| oncoanalyser | Cancer whole-genome and transcriptome analysis (WiGiTS) | 3.0.0 |
| crisprseq | CRISPR gene editing outcomes and screens | 2.3.0 |
| isoseq | PacBio Iso-Seq full-length transcripts | 3.0.1 |
| pairgenomealign | Pairwise genome alignment | 3.0.4 |
| drop | RNA outlier detection: aberrant expression, splicing and mono-allelic expression | 1.0.0 |
| epitopeprediction | MHC binding prediction for variant, protein and peptide inputs | 3.2.0 |
| genomeqc | Genome assembly and annotation QC across genomes | 1.0.1 |
| hlatyping | HLA class I typing with OptiType | 2.2.0 |
| nascent | Nascent transcription time courses (GRO-seq, PRO-seq) | 2.3.0 |
| quantms | Label-free DIA proteomics quantification | 1.1.1 |
| raredisease | Rare disease family analysis: ranked variants and inheritance models | 3.1.2 |
| rnavar | RNA-seq germline variant calling | 1.3.0 |
| stableexpression | Most stable reference genes across public expression data | 1.1.0 |
| viralmetagenome | Viral genome reconstruction from metagenomic reads | 1.2.0 |
You do not have to name the template (v1.10.0+)
A pipeline can trigger the ingestion itself when it completes, and the
template is resolved from the pipeline's own name and version. One command
per machine, then nothing to add to any nextflow run:
See Nextflow trigger.