Subworkflow to run multiple commands in the RSeqC package


Name (Type)

meta (map)

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


bam (file)

BAM file to calculate statistics


bai (file)

Index for input BAM file


bed (file)

BED file for the reference gene model


rseqc_modules (list)

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


Name (Type)

bamstat_txt (file)

bam statistics report


innerdistance_all (file)

All the output files from RSEQC_INNERDISTANCE


innerdistance_distance (file)

the inner distances


innerdistance_freq (file)

frequencies of different insert sizes


innerdistance_mean (file)

mean/median values of inner distances


innerdistance_pdf (file)

distribution plot of inner distances


innerdistance_rscript (file)

script to reproduce the plot


inferexperiment_txt (file)

infer_experiment results report


junctionannotation_all (file)

All the output files from RSEQC_JUNCTIONANNOTATION


junctionannotation_bed (file)

bed file of annotated junctions


junctionannotation_interact_bed (file)

Interact bed file


junctionannotation_xls (file)

xls file with junction information


junctionannotation_pdf (file)

junction plot


junctionannotation_events_pdf (file)

events plot


junctionannotation_rscript (file)

Rscript to reproduce the plots


junctionannotation_log (file)

Log file generated by tool


junctionsaturation_all (file)

All the output files from RSEQC_JUNCTIONSATURATION


junctionsaturation_pdf (file)

Junction saturation report


junctionsaturation_rscript (file)

Junction saturation R-script


readdistribution_txt (file)

the read distribution report


readduplication_all (file)

All the output files from RSEQC_READDUPLICATION


readduplication_seq_xls (file)

Read duplication rate determined from mapping position of read


readduplication_pos_xls (file)

Read duplication rate determined from sequence of read


readduplication_pdf (file)

plot of duplication rate


readduplication_rscript (file)

script to reproduce the plot


tin_txt (file)

TXT file containing results summary


versions (file)

File containing software versions