bam_rseqc

Subworkflow to run multiple commands in the RSeqC package

rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin

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

Description

Subworkflow to run multiple commands in the RSeqC package

Input

name:type

description

pattern

`meta :map`

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

]

`bam :file`

BAM file to calculate statistics

*.{bam}

`bai :file`

Index for input BAM file

*.{bai}

`bed :file`

BED file for the reference gene model

*.{bed}

`rseqc_modules :list`

List of rseqc modules to run
e.g. [ ‘bam_stat’, ‘infer_experiment’ ]

Output

name:type

description

pattern

`bamstat_txt :file`

bam statistics report

*.bam_stat.txt

`innerdistance_all :file`

All the output files from RSEQC_INNERDISTANCE

*.{txt,pdf,R}

`innerdistance_distance :file`

the inner distances

*.inner_distance.txt

`innerdistance_freq :file`

frequencies of different insert sizes

*.inner_distance_freq.txt

`innerdistance_mean :file`

mean/median values of inner distances

*.inner_distance_mean.txt

`innerdistance_pdf :file`

distribution plot of inner distances

*.inner_distance_plot.pdf

`innerdistance_rscript :file`

script to reproduce the plot

*.inner_distance_plot.R

`inferexperiment_txt :file`

infer_experiment results report

*.infer_experiment.txt

`junctionannotation_all :file`

All the output files from RSEQC_JUNCTIONANNOTATION

*.{bed,xls,pdf,R,log}

`junctionannotation_bed :file`

bed file of annotated junctions

*.junction.bed

`junctionannotation_interact_bed :file`

Interact bed file

*.Interact.bed

`junctionannotation_xls :file`

xls file with junction information

*.xls

`junctionannotation_pdf :file`

junction plot

*.junction.pdf

`junctionannotation_events_pdf :file`

events plot

*.events.pdf

`junctionannotation_rscript :file`

Rscript to reproduce the plots

*.r

`junctionannotation_log :file`

Log file generated by tool

*.log

`junctionsaturation_all :file`

All the output files from RSEQC_JUNCTIONSATURATION

*.{pdf,R}

`junctionsaturation_pdf :file`

Junction saturation report

*.pdf

`junctionsaturation_rscript :file`

Junction saturation R-script

*.r

`readdistribution_txt :file`

the read distribution report

*.read_distribution.txt

`readduplication_all :file`

All the output files from RSEQC_READDUPLICATION

*.{xls,pdf,R}

`readduplication_seq_xls :file`

Read duplication rate determined from mapping position of read

*seq.DupRate.xls

`readduplication_pos_xls :file`

Read duplication rate determined from sequence of read

*pos.DupRate.xls

`readduplication_pdf :file`

plot of duplication rate