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3f14b1fabe
* add shovill module * removed deprecated shovill module * fix line ending in functions.nf * fix yaml indentation * reduce spades memory usage * update md5sums * remove non reproducible md5sum * Update test.yml Remove last non-reproducible md5sum. * purely cosmetic order change * proper process label, improve output readability Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: shovill
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## TODO nf-core: Add a description of the module and list keywords
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description: Assemble bacterial isolate genomes from Illumina paired-end reads
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keywords:
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- bacterial
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- assembly
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- illumina
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tools:
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- shovill:
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## TODO nf-core: Add a description and other details for the software below
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description: Microbial assembly pipeline for Illumina paired-end reads
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homepage: https://github.com/tseemann/shovill
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documentation: https://github.com/tseemann/shovill/blob/master/README.md
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licence: ['GPL v2']
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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: List of input paired-end FastQ files
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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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- 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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- contigs:
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type: file
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description: The final assembly produced by Shovill
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pattern: "contigs.fa"
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- corrections:
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type: file
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description: List of post-assembly corrections made by Shovill
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pattern: "shovill.corrections"
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- log:
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type: file
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description: Full log file for bug reporting
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pattern: "shovill.log"
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- raw_contigs:
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type: file
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description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
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pattern: "{skesa,spades,megahit,velvet}.fasta"
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- gfa:
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type: file
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description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet
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pattern: "contigs.{fastg,gfa,LastGraph}"
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authors:
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- "@rpetit3"
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