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