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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
294 lines
10 KiB
YAML
294 lines
10 KiB
YAML
name: vcftools
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description: A set of tools written in Perl and C++ for working with VCF files
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keywords: VCF
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- sort
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tools:
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- vcftools:
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description: A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
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homepage: http://vcftools.sourceforge.net/
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documentation: http://vcftools.sourceforge.net/man_latest.html
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tool_dev_url: None
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doi:
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licence: ["LGPL"]
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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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- variant_file:
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type: file
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description: variant input file which can be vcf, vcf.gz, or bcf format.
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- bed:
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type: file
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description: bed file which can be used with different arguments in vcftools (optional)
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- diff_variant_file:
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type: file
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description: secondary variant file which can be used with the 'diff' suite of tools (optional)
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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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- vcf:
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type: file
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description: vcf file (optional)
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pattern: "*.vcf"
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- bcf:
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type: file
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description: bcf file (optional)
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pattern: "*.bcf"
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- frq:
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type: file
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description: Allele frequency for each site (optional)
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pattern: "*.frq"
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- frq_count:
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type: file
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description: Allele counts for each site (optional)
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pattern: "*.frq.count"
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- idepth:
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type: file
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description: mean depth per individual (optional)
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pattern: "*.idepth"
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- ldepth:
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type: file
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description: depth per site summed across individuals (optional)
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pattern: "*.ildepth"
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- ldepth_mean:
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type: file
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description: mean depth per site calculated across individuals (optional)
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pattern: "*.ldepth.mean"
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- gdepth:
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type: file
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description: depth for each genotype in vcf file (optional)
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pattern: "*.gdepth"
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- hap_ld:
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type: file
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description: r2, D, and D’ statistics using phased haplotypes (optional)
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pattern: "*.hap.ld"
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- geno_ld:
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type: file
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description: squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)
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pattern: "*.geno.ld"
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- geno_chisq:
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type: file
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description: test for genotype independence via the chi-squared statistic (optional)
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pattern: "*.geno.chisq"
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- list_hap_ld:
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type: file
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description: r2 statistics of the sites contained in the provided input file verses all other sites (optional)
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pattern: "*.list.hap.ld"
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- list_geno_ld:
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type: file
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description: r2 statistics of the sites contained in the provided input file verses all other sites (optional)
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pattern: "*.list.geno.ld"
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- interchrom_hap_ld:
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type: file
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description: r2 statistics for sites (haplotypes) on different chromosomes (optional)
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pattern: "*.interchrom.hap.ld"
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- interchrom_geno_ld:
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type: file
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description: r2 statistics for sites (genotypes) on different chromosomes (optional)
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pattern: "*.interchrom.geno.ld"
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- tstv:
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type: file
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description: Transition / Transversion ratio in bins of size defined in options (optional)
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pattern: "*.TsTv"
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- tstv_summary:
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type: file
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description: Summary of all Transitions and Transversions (optional)
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pattern: "*.TsTv.summary"
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- tstv_count:
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type: file
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description: Transition / Transversion ratio as a function of alternative allele count (optional)
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pattern: "*.TsTv.count"
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- tstv_qual:
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type: file
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description: Transition / Transversion ratio as a function of SNP quality threshold (optional)
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pattern: "*.TsTv.qual"
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- filter_summary:
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type: file
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description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)
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pattern: "*.FILTER.summary"
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- sites_pi:
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type: file
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description: Nucleotide divergency on a per-site basis (optional)
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pattern: "*.sites.pi"
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- windowed_pi:
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type: file
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description: Nucleotide diversity in windows, with window size determined by options (optional)
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pattern: "*windowed.pi"
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- weir_fst:
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type: file
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description: Fst estimate from Weir and Cockerham’s 1984 paper (optional)
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pattern: "*.weir.fst"
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- heterozygosity:
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type: file
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description: Heterozygosity on a per-individual basis (optional)
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pattern: "*.het"
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- hwe:
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type: file
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description: Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)
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pattern: "*.hwe"
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- tajima_d:
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type: file
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description: Tajima’s D statistic in bins with size of the specified number in options (optional)
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pattern: "*.Tajima.D"
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- freq_burden:
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type: file
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description: Number of variants within each individual of a specific frequency in options (optional)
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pattern: "*.ifreqburden"
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- lroh:
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type: file
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description: Long Runs of Homozygosity (optional)
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pattern: "*.LROH"
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- relatedness:
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type: file
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description: Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)
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pattern: "*.relatedness"
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- relatedness2:
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type: file
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description: Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)
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pattern: "*.relatedness2"
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- lqual:
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type: file
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description: per-site SNP quality (optional)
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pattern: "*.lqual"
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- missing_individual:
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type: file
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description: Missingness on a per-individual basis (optional)
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pattern: "*.imiss"
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- missing_site:
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type: file
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description: Missingness on a per-site basis (optional)
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pattern: "*.lmiss"
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- snp_density:
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type: file
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description: Number and density of SNPs in bins of size defined by option (optional)
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pattern: "*.snpden"
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- kept_sites:
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type: file
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description: All sites that have been kept after filtering (optional)
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pattern: "*.kept.sites"
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- removed_sites:
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type: file
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description: All sites that have been removed after filtering (optional)
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pattern: "*.removed.sites"
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- singeltons:
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type: file
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description: Location of singletons, and the individual they occur in (optional)
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pattern: "*.singeltons"
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- indel_hist:
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type: file
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description: Histogram file of the length of all indels (including SNPs) (optional)
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pattern: "*.indel_hist"
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- hapcount:
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type: file
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description: Unique haplotypes within user specified bins (optional)
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pattern: "*.hapcount"
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- mendel:
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type: file
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description: Mendel errors identified in trios (optional)
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pattern: "*.mendel"
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- format:
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type: file
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description: Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)
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pattern: "*.FORMAT"
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- info:
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type: file
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description: Extracted information from the INFO field in the VCF file (optional)
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pattern: "*.INFO"
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- genotypes_matrix:
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type: file
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description: |
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Genotypes output as large matrix.
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Genotypes of each individual on a separate line.
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Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.
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Missing genotypes are represented by -1 (optional)
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pattern: "*.012"
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- genotypes_matrix_individual:
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type: file
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description: Details the individuals included in the main genotypes_matrix file (optional)
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pattern: "*.012.indv"
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- genotypes_matrix_position:
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type: file
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description: Details the site locations included in the main genotypes_matrix file (optional)
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pattern: "*.012.pos"
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- impute_hap:
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type: file
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description: Phased haplotypes in IMPUTE reference-panel format (optional)
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pattern: "*.impute.hap"
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- impute_hap_legend:
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type: file
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description: Impute haplotype legend file (optional)
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pattern: "*.impute.hap.legend"
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- impute_hap_indv:
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type: file
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description: Impute haplotype individuals file (optional)
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pattern: "*.impute.hap.indv"
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- ldhat_sites:
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type: file
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description: Output data in LDhat format, sites (optional)
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pattern: "*.ldhat.sites"
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- ldhat_locs:
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type: file
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description: output data in LDhat format, locations (optional)
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pattern: "*.ldhat.locs"
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- beagle_gl:
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type: file
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description: Genotype likelihoods for biallelic sites (optional)
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pattern: "*.BEAGLE.GL"
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- beagle_pl:
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type: file
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description: Genotype likelihoods for biallelic sites (optional)
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pattern: "*.BEAGLE.PL"
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- ped:
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type: file
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description: output the genotype data in PLINK PED format (optional)
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pattern: "*.ped"
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- map_:
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type: file
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description: output the genotype data in PLINK PED format (optional)
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pattern: "*.map"
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- tped:
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type: file
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description: output the genotype data in PLINK PED format (optional)
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pattern: "*.tped"
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- tfam:
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type: file
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description: output the genotype data in PLINK PED format (optional)
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pattern: "*.tfam"
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- diff_sites_in_files:
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type: file
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description: Sites that are common / unique to each file specified in optional inputs (optional)
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pattern: "*.diff.sites.in.files"
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- diff_indv_in_files:
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type: file
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description: Individuals that are common / unique to each file specified in optional inputs (optional)
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pattern: "*.diff.indv.in.files"
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- diff_sites:
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type: file
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description: Discordance on a site by site basis, specified in optional inputs (optional)
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pattern: "*.diff.sites"
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- diff_indv:
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type: file
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description: Discordance on a individual by individual basis, specified in optional inputs (optional)
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pattern: "*.diff.indv"
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- diff_discd_matrix:
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type: file
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description: Discordance matrix between files specified in optional inputs (optional)
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pattern: "*.diff.discordance.matrix"
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- diff_switch_error:
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type: file
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description: Switch errors found between sites (optional)
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pattern: "*.diff.switch"
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authors:
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- "@Mark-S-Hill"
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