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

nf-core/sgdemux @ 0.0.0-0c7146d

Demultiplex bgzip'd fastq files

demultiplex fastq bgzip

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nh13 @sam-white04

Maintainers: @nh13 @sam-white04

Demultiplex bgzip'd fastq files

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

include { SGDEMUX } from 'nf-core/sgdemux'

MIT License

Process

`Name`	`SGDEMUX`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`sample_sheet` file	sample_sheet file (either a Singular Genomics sample sheet, or a two column csv with Sample_Barcode and Sample_ID) `*.{csv}`
`fastqs_dir` directory	Input directory containing bgzipped (not gzip) FASTQ files

Output 7 channels

#1 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/metrics.tsv` file	Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates `${prefix}/metrics.tsv`

#2 sample_fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/_R.fastq.gz` file	Demultiplexed per-sample FASTQ files `${prefix}/_R.fastq.gz`

#3 versions_sgdemux tuple

`${task.process}` string	The name of the process
`sgdemux` string	The name of the tool
`sgdemux --version \| cut -d " " -f2` eval	The expression to obtain the version of the tool

#4 per_sample_metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/per_sample_metrics.tsv` file	Summary metrics for each sample `${prefix}/per_sample_metrics.tsv`

#5 per_project_metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/per_project_metrics.tsv` file	Summary metrics for samples in the same project `${prefix}/per_project_metrics.tsv`

#6 most_frequent_unmatched tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/most_frequent_unmatched.tsv` file	File containing approx. counts of barcodes that did not match the expected barcodes `${prefix}/most_frequence_unmatched.tsv`

#7 sample_barcode_hop_metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/sample_barcode_hop_metrics.tsv` file	File output for dual-indexed runs with barcodes which are unexpected combinations of expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT `${prefix}/sample_barcode_hop_metrics/tsv`

Tool	Description	Homepage
sgdemux	Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.	https://github.com/Singular-Genomics/singular-demux

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:13:36 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsgdemux/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sgdemux/blobs/sha256:e36849035bf4556eada157a37f1f50e76a70bdc1148efd49996a2938ff2f74d2
Size	3.8 KB
Checksum	sha256:e36849035bf4556ead