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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>
54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
name: cnvpytor_importreaddepth
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description: command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.
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keywords:
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- read depth
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- cnv calling
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tools:
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- cnvpytor -rd:
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description: calling CNVs using read depth
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homepage: https://github.com/abyzovlab/CNVpytor
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documentation: https://github.com/abyzovlab/CNVpytor
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tool_dev_url: https://github.com/abyzovlab/CNVpytor
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doi: "10.1101/2021.01.27.428472v1"
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licence: ["MIT"]
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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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- input_file:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram}"
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- index:
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type: file
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description: bam file index
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pattern: "*.{bai,crai}"
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- fasta:
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type: file
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description: specifies reference genome file (only for cram file without reference genome)
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pattern: "*.{fasta,fasta.gz,fa,fa.gz}"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fai"
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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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- pytor:
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type: file
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description: read depth root file in which read depth data binned to 100 base pair bins will be stored.
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pattern: "*.{pytor}"
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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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authors:
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- "@sima-r"
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