Description

Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to ‘link’.

Input

name:type
description
pattern

meta:map

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

]

bam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai:file

BAM index file

*.{bai}

intervals:file

Annotated targets optimized for copy number calling

*.txt

Output

name:type
description
pattern

txt

meta:map

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

]

*.txt.gz:file

Intervals coverage file

*.txt.gz

png

meta:map

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

]

*.png:file

GC-normalized intervals coverage plot. Generated only when GC-normalization is enabled.

*.png

loess_qc_txt

meta:map

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

]

*_loess_qc.txt:file

GC-normalized intervals coverage metrics. Generated only when GC-normalization is enabled.

*_loess_qc.txt

loess_txt

meta:map

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

]

*_loess.txt.gz:file

GC-normalized intervals coverage file. Generated only when GC-normalization is enabled.

*_loess.txt.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

purecn

Copy number calling and SNV classification using targeted short read sequencing

args_id: $args