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https://github.com/MillironX/nf-core_modules.git
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74b569b66a
* Created epang module from template * Module seems to be working * Namechange to epang_place * Move model to meta map * Fix linting problems * Prettier * Forgot --threads! * Moved module to epang * Move reference file params * Directory output * Make all args optional * Added inputs for three other types of file arguments * Update modules/epang/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Add directory to output doc, reorder the other * Make model specification less hardcoded Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
70 lines
2 KiB
YAML
70 lines
2 KiB
YAML
name: "epang"
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description: phylogenetic placement of query sequences in a reference tree
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keywords:
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- phylogeny
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- phylogenetic placement
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- sequences
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tools:
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- "epang":
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description: "Massively parallel phylogenetic placement of genetic sequences"
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homepage: "https://github.com/Pbdas/epa-ng"
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documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
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tool_dev_url: "https://github.com/Pbdas/epa-ng"
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doi: "https://doi.org/10.1093/sysbio/syy054"
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licence: "['GNU Affero General Public License v3.0']"
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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' ]
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- queryaln:
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type: file
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description: aligned query sequences in any supported format including phylip and fasta, may be gzipped
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pattern: "*"
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- referencealn:
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type: file
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description: reference alignment in any supported format including phylip and fasta, may be gzipped
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pattern: "*"
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- referencetree:
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type: file
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description: newick file containing the reference tree in which query sequences will be placed
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pattern: "*"
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- bfastfile:
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type: file
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description: file argument to the --bfast parameter
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pattern: "*"
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- splitfile:
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type: file
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description: file argument to the --split parameter
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pattern: "*"
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- binaryfile:
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type: file
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description: file argument to the --binary parameter
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pattern: "*"
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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' ]
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- epang:
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type: directory
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description: directory in which EPA-NG was run
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- jplace:
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type: file
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description: file with placement information
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pattern: "*.jplace"
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- log:
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type: file
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description: log file from placement
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pattern: "*.log"
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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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- "@erikrikarddaniel"
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