Calls CNVs in bam files from tumor patients
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
normal
:file
BAM files
*.bam
normal_index
BAM file indices
*.bam.bai
tumor
tumor_index
bed
annotated BED file containing target regions
*.bed
fasta
genome FASTA file
*.fasta
png
PNG file containing profile plot
*.profile.png
profile
*.profile.txt
TXT file containing profile data
summary
*.summary.txt
TXT file containing summarized data
versions_oncocnv
${task.process}
:string
The name of the process
oncocnv
The name of the tool
7.0
The expression to obtain the version of the tool
versions_perl
perl
perl --version | sed '2!d;s/.*v//;s/).*//'
:eval
versions_r_base
r-base
R --version | sed '1!d; s/.*version //; s/ .*//'
versions
a package to detect copy number changes in Deep Sequencing data
