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

meta (map)

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

]

txt (file)

Intervals coverage file

*.txt.gz

png (file)

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

*.png

loess_qc_txt (file)

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

*_loess_qc.txt

loess_txt (file)

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

*_loess.txt.gz

versions (file)

File containing software versions

versions.yml
maintainers
Github user aldosr
Github user lbeltrame
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Tools

purecn
Artistic-2.0

Copy number calling and SNV classification using targeted short read sequencing

args_id: $args
bioconductor.org/packages/release/bioc/html/PureCN https://github.com/lima1/PureCN 10.1186/s13029-016-0060-z