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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
49 lines
1.5 KiB
YAML
49 lines
1.5 KiB
YAML
name: qualimap_bamqc
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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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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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- bam:
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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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- use_gff:
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type: boolean
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description: Specifies if feature file should be used or not
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@phue"
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