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15fd90ffe8
* initial stubs [ci skip] * remove comments and add main command [ci skip] * design iteration [ci skip] * add new standard functions.nf [ci skip] * update the version string [ci skip] * accomodate the db stubs and single/double ends [ci skip] * add FIXME for missing info [ci skip] * Accomodate the results folder [ci skip] * Update main.nf * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Add version file to stubs [ci skip] * Tweak the output dir pattern [ci skip] * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
51 lines
1.5 KiB
YAML
51 lines
1.5 KiB
YAML
name: phyloflash
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description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
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keywords:
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- metagenomics
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- illumina datasets
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- phylogenetic composition
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tools:
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- phyloflash:
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description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
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homepage: https://hrgv.github.io/phyloFlash/
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documentation: https://hrgv.github.io/phyloFlash/usage.html
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tool_dev_url: https://github.com/HRGV/phyloFlash
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doi: "10.1128/mSystems.00920-20"
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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', single_end:false ]
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- reads:
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type: file
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description: Channel containing single or paired-end reads
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pattern: "*.{fastq.gz,fq.gz}"
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- sliva_db:
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type: folder
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description: Folder containing the SILVA database
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pattern: "ref"
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- univec_db:
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type: folder
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description: Folder containing UniVec database
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pattern: "UniVec"
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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: folder
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description: Folder containing the results of phyloFlash analysis
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pattern: "${prefix}*"
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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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- "@abhi18av"
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