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51 lines
1.4 KiB
YAML
51 lines
1.4 KiB
YAML
name: qualimap_bamqccram
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description: Evaluate alignment data
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keywords:
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- quality control
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- qc
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- bam
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tools:
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- qualimap:
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description: |
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Qualimap 2 is a platform-independent application written in
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Java and R that provides both a Graphical User Interface and
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a command-line interface to facilitate the quality control of
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alignment sequencing data and its derivatives like feature counts.
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homepage: http://qualimap.bioinfo.cipf.es/
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documentation: http://qualimap.conesalab.org/doc_html/index.html
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doi: 10.1093/bioinformatics/bts503
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licence: ["GPL-2.0-only"]
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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', single_end:false ]
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- bacramm:
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type: file
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description: BAM file
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pattern: "*.{bam}"
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- gff:
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type: file
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description: Feature file with regions of interest
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pattern: "*.{gff,gtf,bed}"
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- fasta:
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type: file
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description: Reference file of cram file
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pattern: "*.{fasta,fa,fna}"
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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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- results:
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type: dir
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description: Qualimap results dir
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pattern: "*/*"
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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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- "@FriederikeHanssen"
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