modules/rustqc

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

rnaseqquality controlqcbamdupradarfeaturecountsrseqcpreseqqualimapsamtools

https://github.com/nf-core/modules/[...]/modules/nf-core/rustqc

Description

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

Input

name:type

description

pattern

`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}

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`gtf`
`:file`

GTF annotation file

*.{gtf}

Output

name:type

description

pattern

`dupradar`

`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/*

`featurecounts`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/featurecounts/*`
`:file`

featureCounts-compatible biotype quantification files

${prefix}/featurecounts/*

`preseq`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/preseq/*`
`:file`

Preseq-compatible library complexity extrapolation

${prefix}/preseq/*

`samtools`

`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/*

`rseqc`

`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/**

`qualimap`

`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/**

`versions_rustqc`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

rustqc
GPL-3.0-or-later

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).

seqeralabs.github.io/RustQC https://github.com/seqeralabs/rustqc

modules/rustqc

Description

Input

meta :map

bam :file

bai :file

meta2 :map

gtf :file

Output

dupradar

meta :map

${prefix}/dupradar/* :file

featurecounts

meta :map

${prefix}/featurecounts/* :file

preseq

meta :map

${prefix}/preseq/* :file

samtools

meta :map

${prefix}/samtools/* :file

rseqc

meta :map

${prefix}/rseqc/** :file

qualimap

meta :map

${prefix}/qualimap/** :file

versions_rustqc

${task.process} :string

rustqc :string

rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p' :eval

Topics

versions

${task.process} :string

rustqc :string

rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p' :eval

Tools

rustqcGPL-3.0-or-later

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`gtf`
`:file`

`dupradar`

`meta`
`:map`

`${prefix}/dupradar/*`
`:file`

`featurecounts`

`meta`
`:map`

`${prefix}/featurecounts/*`
`:file`

`preseq`

`meta`
`:map`

`${prefix}/preseq/*`
`:file`

`samtools`

`meta`
`:map`

`${prefix}/samtools/*`
`:file`

`rseqc`

`meta`
`:map`

`${prefix}/rseqc/**`
`:file`

`qualimap`

`meta`
`:map`

`${prefix}/qualimap/**`
`:file`

`versions_rustqc`

`${task.process}`
`:string`

`rustqc`
`:string`

`rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`rustqc`
`:string`

`rustqc --version 2>&1 | sed -n '1s/rustqc //; 1s/ .*//p'`
`:eval`

rustqc
GPL-3.0-or-later