Depictio Templates
Templates are pre-packaged project configurations that set up a complete bioinformatics analysis project, dashboards included, with a single command.
Available templates¶
16S · ITS · CO1 · 18S amplicon sequencing across Illumina, PacBio, and IonTorrent.
Viral assembly and variant calling — SARS-CoV-2 and other genomes via the nf-core reference config.
Benchmark variant callers against truth sets: precision, recall and F1 for germline small variants, somatic indels and structural variants.
DESeq2 differential expression: per-contrast statistics, gene annotation and the variance-stabilised sample space.
Functional screening of contigs: AMR genes, antimicrobial peptides, biosynthetic gene clusters and CAZymes.
B and T cell repertoire analysis: sequence processing, repertoire composition and clonal analysis.
Gene-fusion detection: caller consensus, per-caller evidence, in-silico validation and splice-junction analysis.
Bulk RNA-seq quantification: MultiQC funnel, Salmon expression overview and a per-gene explorer.
Metagenomic taxonomic profiling across many classifiers, with concordance and confidence views.
Transcription-factor and histone ChIP-seq: MACS3 peaks, HOMER annotation and one consensus set per antibody.
Chromatin accessibility: ataqv library quality, MACS2 broad peaks and the consensus set across libraries.
CUT&RUN / CUT&Tag chromatin profiling: SEACR and MACS2 side by side, their agreement and the consensus set per target.
Ancient DNA: read preprocessing, mapping, damage patterns and contamination estimates to judge authenticity per library and sample.
Hi-C: valid pair statistics, contact maps and compartment and TAD calls, from library QC to 3D genome structure.
Metagenome-assembled genomes: assembly, binning, completeness and contamination, and taxonomy of the recovered bins.
DNA methylation: bisulfite conversion QC, M-bias, CpG coverage and methylation levels compared across samples and groups.
Oxford Nanopore long reads: read length and quality, alignment, and transcript quantification per sample.
Germline and somatic variant calling: alignment QC, variant counts per caller, annotated variants and their genome positions.
Single-cell RNA-seq: barcode ranks, cells called, genes per cell and embeddings of the filtered cells per sample.
Ribosome profiling: footprint lengths, P-site periodicity, ORF calls and translational efficiency against matched RNA-seq.
Small RNA-seq: adapter trimming, read length profiles, miRNA quantification and the contaminant fractions per sample.
De novo genome assembly: contiguity, completeness and assembly QC across assemblers and polishing steps.
Immunopeptidomics: identified MHC peptides, length and anchor-motif signatures, replicate reproducibility and source proteins across runs.
Run demultiplexing: reads per lane and sample, index balance, undetermined barcodes and per-sample quality.
Alternative splicing: differential splicing events and transcript usage between conditions, with the supporting expression.
No template matches that search.
Status levels¶
Generated and not yet reviewed. Expect it to need fixes before it is usable.
Shared as-is. Feedback and PRs welcome.
Tested, CI passes, reviewed by the Depictio team or community.
Validated by the pipeline lead developer. Highest trust level.
How templates work¶
A template bundles:
- Project configuration: workflows, data collections and cross-DC links, with
{VAR_NAME}placeholders - Recipes: Python transforms that turn raw pipeline outputs into dashboard-ready tables
- Dashboard YAML: imported on the first run, with the template variables substituted
- Cross-DC links: interactive filtering across data collections
- Recipe seeds: each recipe's output committed as a
.tsv, so the bundled project can be explored, and re-ingested, without the pipeline run behind it (v1.6.0+)
Contributing a template¶
Want to add a template for another pipeline? The contributing guide covers the directory layout, recipe requirements, and review process.