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* add snippy-core module * Update modules/snippy/core/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/snippy/core/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf * update test Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
67 lines
1.9 KiB
YAML
67 lines
1.9 KiB
YAML
name: snippy_core
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description: Core-SNP alignment from Snippy outputs
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keywords:
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- core
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- alignment
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- bacteria
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- snippy
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tools:
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- snippy:
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description: "Rapid bacterial SNP calling and core genome alignments"
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homepage: "https://github.com/tseemann/snippy"
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documentation: "https://github.com/tseemann/snippy"
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tool_dev_url: "https://github.com/tseemann/snippy"
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doi: ""
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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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- vcf:
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type: file
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description: Annotated variants in VCF format
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pattern: "*.vcf.gz"
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- aligned_fa:
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type: file
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description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
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pattern: "*.aligned.fa.gz"
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- reference:
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type: file
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description: Reference genome in GenBank (preferred) or FASTA format
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pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}"
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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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- 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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- aln:
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type: file
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description: A core SNP alignment in FASTA format
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pattern: "*.aln"
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- full_aln:
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type: file
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description: A whole genome SNP alignment (includes invariant sites)
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pattern: "*.full.aln"
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- tab:
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type: file
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description: Tab-separated columnar list of core SNP sites with alleles but NO annotations
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pattern: "*.tab"
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- vcf:
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type: file
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description: Multi-sample VCF file with genotype GT tags for all discovered alleles
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pattern: "*.vcf"
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- txt:
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type: file
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description: Tab-separated columnar list of alignment/core-size statistics
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pattern: "*.txt"
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authors:
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- "@rpetit3"
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