Nextflow Registry | nf-core/sparsesignatures@0.0.0-0c7146d

nf-core/sparsesignatures @ 0.0.0-0c7146d

mutational signature deconvolution of cancer cells

mutational signatures SBS bs genome reference

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @kdavydzenka @elena-buscaroli

Maintainers: @kdavydzenka @elena-buscaroli

mutational signature deconvolution of cancer cells

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

include { SPARSE_SIGNATURES } from 'nf-core/sparsesignatures'

MIT License

Process

`Name`	`SPARSE_SIGNATURES`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`tsv_join` file	joint tsv file with validated mutations by CNAqc `*.{tsv}`

`genome` string	Reference genome name to use with SparseSignatures (e.g. "GRCh37", "GRCh38")

Output 7 channels

#1 signatures_cv_rds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_cv_means_mse.rds` file	File containing cross-validation results `*{_cv_means_mse.rds}`

#2 signatures_plot_pdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_plot_all.pdf` file	File containing the generated plots `*{_plot_all.pdf}`

#3 signatures_plot_rds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_plot_all.rds` file	File containig the data to generate plots `*{_plot_all.rds}`

#4 signatures_nmfOut_rds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_nmf_Lasso_out.rds` file	File containing the results of nmf LASSO fit (signatures and exposures) `*{_nmf_Lasso_out.rds}`

#5 signatures_bestConf_rds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_best_params_config.rds` file	File containing best parameters configuration (numer of signatures (K) and lambda) `*{_best_params_config.rds}`

#6 signatures_mutCounts_rds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_mut_counts.rds` file	File containing mutational counts across samples/patients `*{_mut_counts.rds}`

#7 versions_sparsesignatures

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
sparsesignatures	SparseSignatures is an R-based computational framework which performs de novo extraction, inference, interpretation, or deconvolution of mutational counts of a large number of patients.	n/a
bsgenome.hsapiens.1000genomes.hs37d5	Reference Genome Sequence (hs37d5), based on NCBI GRCh37	n/a
bsgenome.hsapiens.ucsc.hg38	Full genomic sequences for Homo sapiens (UCSC genome hg38)	n/a

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:16:04 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsparsesignatures/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sparsesignatures/blobs/sha256:5667539682308b70ac0429de05d5caadb3653321285d4d4722b0dd37536774c8
Size	6.7 KB
Checksum	sha256:5667539682308b70ac0429de05d5caadb3653321285d4d4722b0dd37536774c8
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