2021-01-26 15:18:46 +00:00
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name: salmon_quant
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2021-01-26 15:12:41 +00:00
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description: gene/transcript quantification with Salmon
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keywords:
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- index
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- fasta
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- genome
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- reference
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tools:
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- star:
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description: |
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Salmon is a tool for wicked-fast transcript quantification from RNA-seq data
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homepage: https://salmon.readthedocs.io/en/latest/salmon.html
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manual: https://salmon.readthedocs.io/en/latest/salmon.html
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doi: 10.1038/nmeth.4197
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: directory
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description: Folder containing the star index files
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- gtf:
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type: file
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description: GTF of the reference transcriptome
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- transcriptome_fasta:
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type: file
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description: Fasta file of the reference transcriptome
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- alignment_mode:
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type: boolean
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description: whether to run salmon in alignment mode
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output:
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- sample_output:
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type: directory
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description: Folder containing the quantification results for a specific sample
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pattern: "${prefix}"
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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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- "@kevinmenden"
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- "@drpatelh"
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