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{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

BAM index file

*.{bai}

intervals{:bash}

:file

Annotated targets optimized for copy number calling

*.txt

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt.gz{:bash}

:file

Intervals coverage file

*.txt.gz

png{:bash}

meta{:bash}

:map

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

*.png{:bash}

:file

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

*.png

loess_qc_txt{:bash}

meta{:bash}

:map

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

*_loess_qc.txt{:bash}

:file

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

*_loess_qc.txt

loess_txt{:bash}

meta{:bash}

:map

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

*_loess.txt.gz{:bash}

:file

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

*_loess.txt.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

purecn

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
maintainers
Github user aldosr
Github user lbeltrame
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