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aed45dd766
* Add MultiVCFAnalyzer * Fix versions * Fix tests due to md5sum var * Apply suggestions from code review * Linting * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
122 lines
3.7 KiB
YAML
122 lines
3.7 KiB
YAML
name: "multivcfanalyzer"
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description: SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA
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keywords:
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- vcf
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- ancient DNA
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- aDNA
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- SNP
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- GATK UnifiedGenotyper
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- SNP table
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tools:
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- "multivcfanalyzer":
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description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository."
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homepage: "https://github.com/alexherbig/MultiVCFAnalyzer"
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documentation: "https://github.com/alexherbig/MultiVCFAnalyzer"
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tool_dev_url: "https://github.com/alexherbig/MultiVCFAnalyzer"
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doi: "10.1038/nature13591"
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licence: "['GPL >=3']"
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input:
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- vcfs:
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type: file
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description: One or a list of uncompressed VCF file
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pattern: "*.vcf"
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- fasta:
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type: file
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description: Reference genome VCF was generated against
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pattern: "*.{fasta,fna,fa}"
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- snpeff_results:
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type: file
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description: Results from snpEff in txt format (Optional)
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pattern: "*.txt"
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- gff:
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type: file
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description: GFF file corresponding to reference genome fasta (Optional)
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pattern: "*.gff"
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- allele_freqs:
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type: boolean
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description: |
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Whether to include the percentage of reads a given allele is
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present in in the SNP table.
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- genotype_quality:
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type: integer
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description: |
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Minimum GATK genotyping threshold threshold of which a SNP call
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falling under is 'discarded'
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- coverage:
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type: integer
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description: |
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Minimum number of a reads that a position must be covered by to be
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reported
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- homozygous_freq:
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type: number
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description: Fraction of reads a base must have to be called 'homozygous'
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- heterozygous_freq:
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type: mumber
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description: |
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Fraction of which whereby if a call falls above this value, and lower
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than the homozygous threshold, a base will be called 'heterozygous'.
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- gff_exclude:
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type: file
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description: |
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file listing positions that will be 'filtered' (i.e. ignored)
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(Optional)
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pattern: "*.vcf"
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output:
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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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- bam:
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type: file
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description: Sorted BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- full_alignment:
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type: file
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description: Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls
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pattern: ".fasta.gz"
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- info_txt:
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type: file
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description: Information about the run
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pattern: ".txt"
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- snp_alignment:
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type: file
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description: A fasta file of just SNP positions with samples only
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pattern: ".fasta.gz"
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- snp_genome_alignment:
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type: file
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description: A fasta file of just SNP positions with reference genome
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pattern: ".fasta.gz"
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- snpstatistics:
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type: file
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description: Some basic statistics about the SNP calls of each sample
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pattern: ".tsv"
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- snptable:
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type: file
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description: Basic SNP table of combined positions taken from each VCF file
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pattern: ".tsv"
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- snptable_snpeff:
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type: file
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description: Input file for SnpEff
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pattern: ".tsv"
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- snptable_uncertainty:
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type: file
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description: Same as above, but with lower case characters indicating uncertain calls
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pattern: ".tsv"
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- structure_genotypes:
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type: file
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description: Input file for STRUCTURE
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pattern: ".tsv"
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- structure_genotypes_nomissing:
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type: file
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description: Alternate input file for STRUCTURE
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pattern: ".tsv"
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- json:
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type: file
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description: Summary statistics in MultiQC JSON format
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pattern: ".json"
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authors:
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- "@jfy133"
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