Nextflow Registry | nf-core/rustqc@0.0.0-6c4ed3a

nf-core/rustqc @ 0.0.0-6c4ed3a

All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @ewels @pinin4fjords

Maintainers: @ewels @pinin4fjords

All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats

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

include { RUSTQC } from 'nf-core/rustqc'

MIT License

Process

`Name`	`RUSTQC`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Sorted BAM file `*.{bam}`
`bai` file	BAM index file `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`gtf` file	GTF annotation file `*.{gtf}`

Output 7 channels

#1 rseqc tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/rseqc/**` file	RSeQC-compatible outputs (bam_stat, infer_experiment, read_distribution, read_duplication, junction_annotation, junction_saturation, inner_distance, TIN) `${prefix}/rseqc/**`

#2 preseq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/preseq/*` file	Preseq-compatible library complexity extrapolation `${prefix}/preseq/*`

#3 dupradar tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/dupradar/*` file	dupRadar-compatible duplication rate plots and tables `${prefix}/dupradar/*`

#4 qualimap tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/qualimap/**` file	Qualimap RNA-seq QC report and raw data `${prefix}/qualimap/**`

#5 samtools tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/samtools/*` file	SAMtools flagstat, idxstats, and stats output `${prefix}/samtools/*`

#6 featurecounts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/featurecounts/*` file	featureCounts-compatible biotype quantification files `${prefix}/featurecounts/*`

#7 versions_rustqc tuple

`${task.process}` string	The process the versions were collected from
`rustqc` string	The tool name
`rustqc --version 2>&1 \| sed -n '1s/rustqc //; 1s/ .*//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
rustqc	RustQC is a high-performance, Rust-based tool that replaces multiple post-alignment RNA-seq QC tools in a single pass over the BAM file. It produces output compatible with MultiQC for dupRadar, featureCounts biotype QC, RSeQC (bam_stat, infer_experiment, read_distribution, read_duplication, junction_annotation, junction_saturation, inner_distance, TIN), Preseq, Qualimap, and SAMtools (flagstat, idxstats, stats).	https://seqeralabs.github.io/RustQC/