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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
1.6 KiB
YAML
57 lines
1.6 KiB
YAML
name: shovill
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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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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: "versions.yml"
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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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