Nextflow Registry | nf-core/mirtrace/qc@0.0.0-6c4ed3a

nf-core/mirtrace/qc @ 0.0.0-6c4ed3a

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

microRNA smrnaseq QC

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:30:55 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fmirtrace%2Fqc/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/mirtrace/qc/blobs/sha256:9015761877ac871e5817ba351fb9b7388c5f4ce268d5cc13dc7462a170f96558
Size	4.0 KB
Checksum	sha256:9015761877ac871e5817ba351fb9b7388c5f4ce268d5cc13dc7462a170f96558
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:30:55 (UTC)		3	4.0 KB