×

nf-core/tinc @ 0.0.0-76dfaba

TINC is a package to determine the contamination of tumour DNA in a matched normal sample. The approach uses evolutionary theory applied to read counts data from whole-genome sequencing assays.

genomics tumour contamination normal purity
Latest version: 0.0.0-76dfaba
Total downloads: 0
Source: nf-core/modules
Authors: @valerianilucrezia
Maintainers: @valerianilucrezia

Summary

TINC is a package to determine the contamination of tumour DNA in a matched normal sample. The approach uses evolutionary theory applied to read counts data from whole-genome sequencing assays.

Get started

Add the following snippet to your workflow script to include this module.

include { TINC } from 'nf-core/tinc'

License

MIT License

Process
Name TINC
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]
cna_rds file

RDS file with copy number segments and purity
vcf_rds file

RDS file with vcf calls from tumour and normal sample
Output 5 channels
#1 rds tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]
*_fit.rds file

RDS file with the fit results

 *.{rds}
#2 plot_pdf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]
*.pdf file

PDF file with the plot of the results

 *.{pdf}
#3 plot_rds tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]
*_plot.rds file

RDS file with the plot of the results

 *.{rds}
#4 tinc_csv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', tumour_sample:'tumour_sample1_name', normal_sample:'normal_sample_name' ]
*_qc.csv file

CSV file with the output of TINC qc flag

 *.{csv}
#5 versions_tinc
versions.yml file

File containing software versions

 versions.yml
Tool Description Homepage
tinc TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses. https://caravagnalab.github.io/TINC/
Version 0.0.0-76dfaba
Commit ID 76dfaba27ac4eacd80cdac5ba28985ee2646b0bd
Release Date 27 May 2026 15:00:58 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Ftinc/0.0.0-76dfaba/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/tinc/blobs/sha256:36cb29ca315dbbeb46776e25a71897ee86baa7208d9057994bf3c59c397c8475
Size 4.6 KB
Checksum sha256:36cb29ca315dbbeb46776e25a71897ee86baa7208d9057994bf3c59c397c8475
Downloads 0
Version Date Status Downloads Size Diff
0.0.0-76dfaba 27 May 2026 15:00:58 (UTC) 0 4.6 KB ↔
0.0.0-6c4ed3a 23 Apr 2026 15:49:55 (UTC) 0 4.3 KB ↔
0.0.0-3fc6d40 22 Apr 2026 15:34:32 (UTC) 0 4.4 KB ↔