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110 lines
3.2 KiB
YAML
110 lines
3.2 KiB
YAML
name: snippy_run
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description: Rapid haploid variant calling
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keywords:
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- variant
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- fastq
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- bacteria
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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- index:
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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,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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- tab:
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type: file
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description: A simple tab-separated summary of all the variants
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pattern: "*.tab"
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- csv:
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type: file
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description: A comma-separated version of the .tab file
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pattern: "*.csv"
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- html:
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type: file
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description: A HTML version of the .tab file
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pattern: "*.html"
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- vcf:
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type: file
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description: The final annotated variants in VCF format
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pattern: "*.vcf"
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- bed:
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type: file
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description: The variants in BED format
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pattern: "*.bed"
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- gff:
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type: file
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description: The variants in GFF3 format
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pattern: "*.gff"
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- bam:
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type: file
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description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
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pattern: "*.bam"
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- bai:
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type: file
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description: Index for the .bam file
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pattern: "*.bam.bai"
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- log:
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type: file
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description: A log file with the commands run and their outputs
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pattern: "*.log"
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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"
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- consensus_fa:
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type: file
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description: A version of the reference genome with all variants instantiated
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pattern: "*.consensus.fa"
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- consensus_subs_fa:
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type: file
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description: A version of the reference genome with only substitution variants instantiated
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pattern: "*.consensus.subs.fa"
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- raw_vcf:
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type: file
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description: The unfiltered variant calls from Freebayes
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pattern: "*.raw.vcf"
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- filt_vcf:
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type: file
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description: The filtered variant calls from Freebayes
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pattern: "*.filt.vcf"
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- vcf_gz:
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type: file
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description: Compressed .vcf file via BGZIP
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pattern: "*.vcf.gz"
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- vcf_csi:
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type: file
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description: Index for the .vcf.gz via bcftools index
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pattern: "*.vcf.gz.csi"
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- txt:
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type: file
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description: Tab-separated columnar list of statistics
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pattern: "*.txt"
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authors:
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- "@rpetit3"
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