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70 lines
2.3 KiB
YAML
70 lines
2.3 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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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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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