Nextflow Registry | nf-core/ichorcna/run@0.0.0-6c4ed3a

nf-core/ichorcna/run @ 0.0.0-6c4ed3a

ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA

ichorcna cnv cna cfDNA wgs

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @sppearce @adamrtalbot

Maintainers: @sppearce @adamrtalbot

ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA

Add the following snippet to your workflow script to include this module.

include { ICHORCNA_RUN } from 'nf-core/ichorcna/run'

MIT License

Process

`Name`	`ICHORCNA_RUN`

Input 8 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`wig` file	hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window `*.{wig}`

`gc_wig` file	hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window `*.{wig}`

`map_wig` file	hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window `*.{wig}`

`normal_wig` file	hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window `*.{wig}`

`normal_background` file	Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc. `*.{rds}`

`centromere` file	Text file giving centromere locations of each genome, to exclude these windows `*.{txt}`

`rep_time_wig` file	Replication/timing .wig file. `*.{wig}`

`exons` file	BED file for exon regions to annotate CNA regions. `*.{bed}`

Output 9 channels

#1 seg tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}.seg` file	Predicted copy number variation per segment `*.{seg}`

#2 plots tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/*.pdf` file	Plots with e.g. individual chromosomes and different considered ploidy `*.{pdf}`

#3 rdata tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}.RData` file	RData file containing all the intermediate R objects `*.{cng.seg}`

#4 cna_seg tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}.cna.seg` file	Predicted copy number variation per segment `*.{cng.seg}`

#5 seg_txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}.seg.txt` file	Predicted copy number variation per segment `*.{seg.txt}`

#6 versions

`versions.yml` file	File containing software versions `versions.yml`

#7 genome_plot tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`**/${prefix}_genomeWide.pdf` file	A plot with the best-fit genome-wide CNV data `*.{genomeWide.pdf}`

#8 corrected_depth tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}.correctedDepth.txt` file	A text file with corrected depth per bin `*.{params.txt}`