Description

Calls CNVs in bam files from tumor patients

Input

Name (Type)
Description
Pattern

meta (map)

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

]

normal (file)

BAM files

*.bam

normal_index (file)

BAM file indices

*.bam.bai

tumor (file)

BAM files

*.bam

tumor_index (file)

BAM file indices

*.bam.bai

bed (file)

annotated BED file containing target regions

*.bed

fasta (file)

genome FASTA file

*.fasta

Output

Name (Type)
Description
Pattern

png (file)

PNG file containing profile plot

*.profile.png

profile (file)

TXT file containing profile data

*.profile.txt

summary (file)

TXT file containing summarized data

*.summary.txt

versions (file)

File containing software versions

versions.yml