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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
61 lines
1.5 KiB
YAML
61 lines
1.5 KiB
YAML
name: deeptools_plotfingerprint
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description: plots cumulative reads coverages by BAM file
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keywords:
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- plot
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- fingerprint
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- cumulative coverage
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- bam
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tools:
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- deeptools:
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description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
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homepage:
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documentation: https://deeptools.readthedocs.io/en/develop/index.html
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tool_dev_url: https://github.com/deeptools/deepTools
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doi: "10.1093/nar/gku365"
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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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- bam:
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type: file
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description: One or more BAM files
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pattern: "*.{bam}"
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- bais:
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type: file
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description: Corresponding BAM file indexes
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pattern: "*.bam.bai"
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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', single_end:false ]
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- pdf:
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type: file
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description: |
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Output figure containing resulting plot
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pattern: "*.{plotFingerprint.pdf}"
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- matrix:
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type: file
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description: |
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Output file summarizing the read counts per bin
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pattern: "*.{plotFingerprint.raw.txt}"
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- metrics:
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type: file
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description: |
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file containing BAM file quality metrics
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pattern: "*.{qcmetrics.txt}"
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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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- "@emiller88"
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- "@drpatelh"
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- "@joseespinosa"
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