nf-core_modules/modules/ichorcna/run/meta.yml

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name: ichorcna_run
description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA
keywords:
- ichorcna
- cnv
- cna
- cfDNA
- wgs
tools:
- ichorcna:
description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
homepage: https://github.com/broadinstitute/ichorCNA
documentation: https://github.com/broadinstitute/ichorCNA/wiki
tool_dev_url: https://github.com/broadinstitute/ichorCNA
doi: "10.1038/s41467-017-00965-y"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- wig:
type: file
description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window
pattern: "*.{wig}"
- gc_wig:
type: file
description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window
pattern: "*.{wig}"
- map_wig:
type: file
description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window
pattern: "*.{wig}"
- panel_of_normals:
type: file
description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc.
pattern: "*.{rds}"
- centromere:
type: file
description: Text file giving centromere locations of each genome, to exclude these windows
pattern: "*.{txt}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- cna_seg:
type: file
description: Predicted copy number variation per segment
pattern: "*.{cng.seg}"
- ichorcna_params:
type: file
description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc
pattern: "*.{params.txt}"
- genome_plot:
type: file
description: A plot with the best-fit genome-wide CNV data
pattern: "*.{genomeWide.pdf}"
authors:
- "@sppearce"