modules/purecn_normaldb

Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.

copy number alteration callingnormal databasepanel of normalshybrid capture sequencingtargeted sequencingDNA sequencing

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`coverage_files`
`:file`

Coverage files from normal samples

*.txt.gz

`normal_vcf`
`:file`

Normal panel in VCF format, used to precompute mapping bias for faster runtimes. Optional.

*.vcf.gz

`normal_vcf_tbi`
`:file`

Normal panel in VCF format

*.vcf.gz.tbi

`genome`
`:string`

Genome build

`assay`
`:string`

Assay name

Output

name:type

description

pattern

`rds`

`meta`
`:file`

File containing the generated panel of normals

normalDB*.rds

`normalDB*.rds`
`:file`

File containing the generated panel of normals

normalDB*.rds

`png`

`meta`
`:file`

File containing the generated panel of normals

normalDB*.rds

`interval_weights*.png`
`:file`

Plot of interval weights calculated from the panel of normals

interval_weights*.png

`bias_rds`

`meta`
`:file`

File containing the generated panel of normals

normalDB*.rds

`mapping_bias*.rds`
`:file`

Calculated mapping bias from the normal files

mapping_bias*.rds

`bias_bed`

`meta`
`:file`

File containing the generated panel of normals

normalDB*.rds

`mapping_bias_hq_sites*.bed`
`:file`

Calculated mapping bias sites from the normal files

mapping_bias_hq_sites*.bed

`low_cov_bed`

`meta`
`:file`

File containing the generated panel of normals

normalDB*.rds

`low_coverage_targets*.bed`
`:file`

BED with possibly low coverage targets identified, only generated if there are low coverage targets

low_coverage_targets*.bed

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

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

modules/purecn_normaldb

Description

Input

`meta`
`:map`

`coverage_files`
`:file`

`normal_vcf`
`:file`

`normal_vcf_tbi`
`:file`

`genome`
`:string`

`assay`
`:string`

Output

`rds`

`meta`
`:file`

`normalDB*.rds`
`:file`

`png`

`meta`
`:file`

`interval_weights*.png`
`:file`

`bias_rds`

`meta`
`:file`

`mapping_bias*.rds`
`:file`

`bias_bed`

`meta`
`:file`

`mapping_bias_hq_sites*.bed`
`:file`

`low_cov_bed`

`meta`
`:file`

`low_coverage_targets*.bed`
`:file`

`versions`

`versions.yml`
`:file`

Tools

purecn
Artistic-2.0

maintainers

get in touch

modules/purecn_normaldb

Description

Input

meta:map

coverage_files:file

normal_vcf:file

normal_vcf_tbi:file

genome:string

assay:string

Output

rds

meta:file

normalDB*.rds:file

png

meta:file

interval_weights*.png:file

bias_rds

meta:file

mapping_bias*.rds:file

bias_bed

meta:file

mapping_bias_hq_sites*.bed:file

low_cov_bed

meta:file

low_coverage_targets*.bed:file

versions

versions.yml:file

Tools

purecn Artistic-2.0

maintainers

get in touch

`meta`
`:map`

`coverage_files`
`:file`

`normal_vcf`
`:file`

`normal_vcf_tbi`
`:file`

`genome`
`:string`

`assay`
`:string`

`rds`

`meta`
`:file`

`normalDB*.rds`
`:file`

`png`

`meta`
`:file`

`interval_weights*.png`
`:file`

`bias_rds`

`meta`
`:file`

`mapping_bias*.rds`
`:file`

`bias_bed`

`meta`
`:file`

`mapping_bias_hq_sites*.bed`
`:file`

`low_cov_bed`

`meta`
`:file`

`low_coverage_targets*.bed`
`:file`

`versions`

`versions.yml`
`:file`

purecn
Artistic-2.0