bam_qc_rnaseq

Run post-alignment QC tools on RNA-seq BAM files including library complexity estimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics (Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis.

rnaseqbamqcquality_controlpreseqqualimapdupradarrseqcfeaturecountsbiotype

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

Description

Input

name

description

pattern

`meta`

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

`bam`

Coordinate-sorted BAM file aligned to the genome

*.{bam}

`bai`

Index for the genome-aligned BAM file

*.{bai}

`gtf`

GTF annotation file

*.{gtf}

`gene_bed`

BED12 file for the reference gene model

*.{bed}

`fasta_fai`

Tuple of FASTA and FAI files for samtools sort
[ val(meta), path(fasta), path(fai) ]

`biotypes_header`

Header file for biotype counts MultiQC section

*.{txt}

`tools`

List of QC tools to run. Top-level tools: ‘preseq’, ‘biotype_qc’, ‘qualimap’,
‘dupradar’. RSeQC modules use an ‘rseqc_’ prefix: ‘rseqc_bam_stat’,
‘rseqc_inner_distance’, ‘rseqc_infer_experiment’, ‘rseqc_junction_annotation’,
‘rseqc_junction_saturation’, ‘rseqc_read_distribution’, ‘rseqc_read_duplication’,
‘rseqc_tin’. Pass an empty list to skip all.

`biotype`

GTF attribute for biotype grouping (e.g. “gene_type” or “gene_biotype”).
Only used when ‘biotype_qc’ is in tools. Set to empty string to skip biotype QC.

Output

name

description

pattern

`multiqc_files`

Collected MultiQC-compatible output files from all enabled tools

`preseq_lc_extrap`

Preseq library complexity extrapolation curve

*.lc_extrap.txt

`preseq_log`

Preseq log file

*.log

`featurecounts_counts`

featureCounts count matrix

*.featureCounts.txt

`featurecounts_summary`

featureCounts summary statistics

*.featureCounts.txt.summary

`biotype_tsv`

Biotype counts formatted for MultiQC bargraph

*biotype_counts_mqc.tsv

`biotype_rrna`

rRNA percentage for MultiQC general stats

*biotype_counts_rrna_mqc.tsv

`qualimap_results`

Qualimap RNA-seq QC results directory

`dupradar_multiqc`

dupRadar MultiQC-compatible output

*_mqc.txt

`inferexperiment_txt`

RSeQC infer_experiment results (for strandedness detection)

*.infer_experiment.txt

`bamstat_txt`

RSeQC bam_stat report

*.bam_stat.txt

`readdistribution_txt`

RSeQC read_distribution report

*.read_distribution.txt

`tin_txt`

RSeQC TIN results summary

*.txt