modules/purecn_coverage

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

copy number alteration callingintervals coveragehybrid capture sequencingtargeted sequencingDNA sequencing

https://github.com/nf-core/modules/[...]/modules/nf-core/purecn/coverage

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

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

modules/purecn_coverage

Description

Input

`meta:map`

`bam:file`

`bai:file`

`intervals:file`

Output

`txt`

`meta:map`

`*.txt.gz:file`

`png`

`meta:map`

`*.png:file`

`loess_qc_txt`

`meta:map`

`*_loess_qc.txt:file`

`loess_txt`

`meta:map`

`*_loess.txt.gz:file`

`versions`

`versions.yml:file`

Tools

purecn

maintainers

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