nf-core_modules/modules/snippy/run/meta.yml
2022-05-10 21:47:57 +00:00

110 lines
3.2 KiB
YAML

name: snippy_run
description: Rapid haploid variant calling
keywords:
- variant
- fastq
- bacteria
tools:
- snippy:
description: "Rapid bacterial SNP calling and core genome alignments"
homepage: "https://github.com/tseemann/snippy"
documentation: "https://github.com/tseemann/snippy"
tool_dev_url: "https://github.com/tseemann/snippy"
doi: ""
licence: "['GPL v2']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- index:
type: file
description: Reference genome in GenBank (preferred) or FASTA format
pattern: "*.{gbk,gbk.gz,fa,fa.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- tab:
type: file
description: A simple tab-separated summary of all the variants
pattern: "*.tab"
- csv:
type: file
description: A comma-separated version of the .tab file
pattern: "*.csv"
- html:
type: file
description: A HTML version of the .tab file
pattern: "*.html"
- vcf:
type: file
description: The final annotated variants in VCF format
pattern: "*.vcf"
- bed:
type: file
description: The variants in BED format
pattern: "*.bed"
- gff:
type: file
description: The variants in GFF3 format
pattern: "*.gff"
- bam:
type: file
description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
pattern: "*.bam"
- bai:
type: file
description: Index for the .bam file
pattern: "*.bam.bai"
- log:
type: file
description: A log file with the commands run and their outputs
pattern: "*.log"
- aligned_fa:
type: file
description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
pattern: "*.aligned.fa"
- consensus_fa:
type: file
description: A version of the reference genome with all variants instantiated
pattern: "*.consensus.fa"
- consensus_subs_fa:
type: file
description: A version of the reference genome with only substitution variants instantiated
pattern: "*.consensus.subs.fa"
- raw_vcf:
type: file
description: The unfiltered variant calls from Freebayes
pattern: "*.raw.vcf"
- filt_vcf:
type: file
description: The filtered variant calls from Freebayes
pattern: "*.filt.vcf"
- vcf_gz:
type: file
description: Compressed .vcf file via BGZIP
pattern: "*.vcf.gz"
- vcf_csi:
type: file
description: Index for the .vcf.gz via bcftools index
pattern: "*.vcf.gz.csi"
- txt:
type: file
description: Tab-separated columnar list of statistics
pattern: "*.txt"
authors:
- "@rpetit3"