mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 19:48:16 +00:00
78e2e76b24
* hmmcopy/mapCounter * update test * Remove bam tag * Remove /tmp/ path from test.yml * Update modules/hmmcopy/mapcounter/meta.yml Incorporate formatting changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/hmmcopy/mapcounter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/hmmcopy/mapcounter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * ichorCNA run * Add panel of normals code * Try and fix tests * Edit string detection in tests * Fix linting issues * Just failing END_VERSIONS * Fixed versions.yml * Added DOI * Optional name for file * Add when command * Updated when * Update modules/ichorcna/createpon/main.nf Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
72 lines
2.3 KiB
YAML
72 lines
2.3 KiB
YAML
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"
|