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f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
57 lines
1.9 KiB
YAML
57 lines
1.9 KiB
YAML
name: ichorcna_createpon
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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. This module generates a panel of normals
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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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- panel_of_normals
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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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- wigs:
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type: file
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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.
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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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- 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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- 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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- rds:
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type: file
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description: R data file (.rds) containing panel of normals data, medians of each bin.
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pattern: "*.rds"
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- txt:
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type: file
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description: Text file containing panel of normals data, medians of each bin.
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pattern: "*.txt"
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authors:
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- "@sppearce"
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