nf-core_modules/modules/ichorcna/createpon/meta.yml
Edmund Miller f080015754
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Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 14:27:50 +01:00

57 lines
1.9 KiB
YAML

name: ichorcna_createpon
description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals
keywords:
- ichorcna
- cnv
- cna
- cfDNA
- wgs
- panel_of_normals
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:
- wigs:
type: file
description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals.
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}"
- centromere:
type: file
description: Text file giving centromere locations of each genome, to exclude these windows
pattern: "*.{txt}"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- rds:
type: file
description: R data file (.rds) containing panel of normals data, medians of each bin.
pattern: "*.rds"
- txt:
type: file
description: Text file containing panel of normals data, medians of each bin.
pattern: "*.txt"
authors:
- "@sppearce"