Nextflow Registry | nf-core/mirtrace/qc@0.0.0-0c7146d

nf-core/mirtrace/qc @ 0.0.0-0c7146d

A tool for quality control and tracing taxonomic origins of microRNA sequencing data

microRNA smrnaseq QC

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @atrigila

Maintainers: @atrigila

A tool for quality control and tracing taxonomic origins of microRNA sequencing data

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

include { MIRTRACE_QC } from 'nf-core/mirtrace/qc'

MIT License

Process

`Name`	`MIRTRACE_QC`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	microRNA sequencing data `*.{fastq,fastq.gz}`
`mirtrace_config` file	(Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns "FASTQ file path, id, adapter, PHRED-ASCII-offset".

`mirtrace_species` string	Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens)

Output 6 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.tsv` file	TSV file `*.{tsv}`

#2 html tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.html` file	HTML file `*.{html}`

#3 json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.json` file	JSON file `*.{json}`

#4 all_fa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`qc_passed_reads.all.collapsed/*.{fa,fasta}` file	QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. `*.{fa,fasta}`

#5 versions

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

#6 rnatype_unknown_fa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}` file	Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. `*.{fa,fasta}`

Tool	Description	Homepage
mirtrace	miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.	https://github.com/friedlanderlab/mirtrace/tree/master

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:56:13 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmirtrace%2Fqc/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/mirtrace/qc/blobs/sha256:c9bd48b580ce7d57e54ad9f9458d8e8d6bac01ddeb7e75393fee70a94fbedf04
Size	4.1 KB
Checksum	sha256:c9bd48b580ce7d57e54ad9f9458d8e8d6bac01ddeb7e75393fee70a94fbedf04
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:56:13 (UTC)		1