modules/purecn_run

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

copy number alteration callinghybrid capture sequencingtargeted sequencingDNA sequencing

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

Description

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

Input

name:type

description

pattern

`meta:map`

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

`intervals:file`

BED file of target intervals, generated from IntervalFile.R

{*.bed,*.txt}

`coverage:file`

Coverage file generated from Coverage.R

*.txt

`normal_db:file`

normal pannel database

`genome:string`

Genome build

Output

name:type

description

pattern

`pdf`

`meta:file`

PDF file containing copy number plots

*.pdf

`*.pdf:file`

PDF file containing copy number plots

*.pdf

`local_optima_pdf`

`meta:file`

PDF file containing local optima plots

*_local_optima.pdf

`*_local_optima.pdf:file`

PDF file containing local optima plots

*_local_optima.pdf

`seg`

`meta:file`

Tab-delimited file containing segmentation results

*_dnacopy.seg

`*_dnacopy.seg:file`

Tab-delimited file containing segmentation results

*_dnacopy.seg

`genes_csv`

`meta:file`

CSV file containing gene copy number calls. Optional

*_genes.csv

`*_genes.csv:file`

CSV file containing gene copy number calls. Optional

*_genes.csv

`amplification_pvalues_csv`

`meta:file`

CSV file containing amplification p-values. Optional

*_amplification_pvalues.csv

`*_amplification_pvalues.csv:file`

CSV file containing amplification p-values. Optional

*_amplification_pvalues.csv

`ues_csv:file`

CSV file containing amplification p-values. Optional

*_amplification_pvalues.csv

`vcf_gz`

`meta:file`

GZipped VCF file containing SNV calls. Optional

*.vcf.gz

`*.vcf.gz:file`

GZipped VCF file containing SNV calls. Optional

*.vcf.gz

`variants_csv`

`meta:file`

CSV file containing SNV calls. Optional

*_variants.csv

`*_variants.csv:file`

CSV file containing SNV calls. Optional

*_variants.csv

`loh_csv`

`meta:file`

CSV file containing LOH calls. Optional

*_loh.csv

`*_loh.csv:file`

CSV file containing LOH calls. Optional

*_loh.csv

`chr_pdf`

`meta:file`

PDF file containing chromosome plots. Optional

*_chromosomes.pdf

`*_chromosomes.pdf:file`

PDF file containing chromosome plots. Optional

*_chromosomes.pdf

`segmentation_pdf`

`meta:file`

PDF file containing segmentation plots. Optional

*_segmentation.pdf

`*_segmentation.pdf:file`

PDF file containing segmentation plots. Optional

*_segmentation.pdf

`multisample_seg`

`meta:map`

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

`*_multisample.seg:file`

multisample segmentation results

*_multisample.seg

`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_run

Description

Input

meta:map

intervals:file

coverage:file

normal_db:file

genome:string

Output

pdf

meta:file

*.pdf:file

local_optima_pdf

meta:file

*_local_optima.pdf:file

seg

meta:file

*_dnacopy.seg:file

genes_csv

meta:file

*_genes.csv:file

amplification_pvalues_csv

meta:file

*_amplification_pvalues.csv:file

ues_csv:file

vcf_gz

meta:file

*.vcf.gz:file

variants_csv

meta:file

*_variants.csv:file

loh_csv

meta:file

*_loh.csv:file

chr_pdf

meta:file

*_chromosomes.pdf:file

segmentation_pdf

meta:file

*_segmentation.pdf:file

multisample_seg

meta:map

*_multisample.seg:file

versions

versions.yml:file

Tools

purecn

maintainers

get in touch

`meta:map`

`intervals:file`

`coverage:file`

`normal_db:file`

`genome:string`

`pdf`

`meta:file`

`*.pdf:file`

`local_optima_pdf`

`meta:file`

`*_local_optima.pdf:file`

`seg`

`meta:file`

`*_dnacopy.seg:file`

`genes_csv`

`meta:file`

`*_genes.csv:file`

`amplification_pvalues_csv`

`meta:file`

`*_amplification_pvalues.csv:file`

`ues_csv:file`

`vcf_gz`

`meta:file`

`*.vcf.gz:file`

`variants_csv`

`meta:file`

`*_variants.csv:file`

`loh_csv`

`meta:file`

`*_loh.csv:file`

`chr_pdf`

`meta:file`

`*_chromosomes.pdf:file`

`segmentation_pdf`

`meta:file`

`*_segmentation.pdf:file`

`multisample_seg`

`meta:map`

`*_multisample.seg:file`

`versions`

`versions.yml:file`