Description

Run PureCN workflow to normalize, segment and determine purity and ploidy

Input

name:type
description
pattern

meta{:bash}

:map

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

intervals{:bash}

:file

BED file of target intervals, generated from IntervalFile.R

{*.bed,*.txt}

coverage{:bash}

:file

Coverage file generated from Coverage.R

*.txt

vcf{:bash}

:file

VCF containing variant calls

*.vcf.gz

normal_db{:bash}

:file

Normal panel database

mapping_bias{:bash}

:file

Mapping bias file generated with normal panel

genome{:bash}

:string

Genome build

Output

name:type
description
pattern

pdf{:bash}

meta{:bash}

:map

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

*.pdf{:bash}

:file

PDF file containing copy number plots

*.pdf

local_optima_pdf{:bash}

meta{:bash}

:map

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

*_local_optima.pdf{:bash}

:file

PDF file containing local optima plots

*_local_optima.pdf

seg{:bash}

meta{:bash}

:map

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

*_dnacopy.seg{:bash}

:file

Tab-delimited file containing segmentation results

*_dnacopy.seg

csv{:bash}

meta{:bash}

:map

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

${prefix}.csv{:bash}

:file

Tab-delimited file containing sample purity, ploidy and flags information

${prefix}.csv

genes_csv{:bash}

meta{:bash}

:map

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

*_genes.csv{:bash}

:file

CSV file containing gene copy number calls. Optional

*_genes.csv

amplification_pvalues_csv{:bash}

meta{:bash}

:map

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

*_amplification_pvalues.csv{:bash}

:file

CSV file containing amplification p-values. Optional

*_amplification_pvalues.csv

vcf_gz{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

GZipped VCF file containing SNV calls. Optional

*.vcf.gz

variants_csv{:bash}

meta{:bash}

:map

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

*_variants.csv{:bash}

:file

CSV file containing SNV calls. Optional

*_variants.csv

loh_csv{:bash}

meta{:bash}

:map

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

*_loh.csv{:bash}

:file

CSV file containing LOH calls. Optional

*_loh.csv

chr_pdf{:bash}

meta{:bash}

:map

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

*_chromosomes.pdf{:bash}

:file

PDF file containing chromosome plots. Optional

*_chromosomes.pdf

segmentation_pdf{:bash}

meta{:bash}

:map

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

*_segmentation.pdf{:bash}

:file

PDF file containing segmentation plots. Optional

*_segmentation.pdf

multisample_seg{:bash}

meta{:bash}

:map

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

*_multisample.seg{:bash}

:file

multisample segmentation results

*_multisample.seg

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Log file of the analysis

*.log

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
get in touch
Ask a question on Slack Open an issue on GitHub