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Fixing tests
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3 changed files with 4 additions and 68 deletions
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@ -1,64 +0,0 @@
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# This file was produced by bcftools stats (1.11+htslib-1.11) and can be plotted using plot-vcfstats.
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# The command line was: bcftools stats test.vcf
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#
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# Definition of sets:
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# ID [2]id [3]tab-separated file names
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ID 0 test.vcf
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# SN, Summary numbers:
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# number of records .. number of data rows in the VCF
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# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
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# number of SNPs .. number of rows with a SNP
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# number of MNPs .. number of rows with a MNP, such as CC>TT
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# number of indels .. number of rows with an indel
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# number of others .. number of rows with other type, for example a symbolic allele or
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# a complex substitution, such as ACT>TCGA
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# number of multiallelic sites .. number of rows with multiple alternate alleles
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# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
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#
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# Note that rows containing multiple types will be counted multiple times, in each
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# counter. For example, a row with a SNP and an indel increments both the SNP and
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# the indel counter.
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#
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# SN [2]id [3]key [4]value
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SN 0 number of samples: 1
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SN 0 number of records: 15
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SN 0 number of no-ALTs: 2
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SN 0 number of SNPs: 7
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SN 0 number of MNPs: 0
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SN 0 number of indels: 3
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SN 0 number of others: 3
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SN 0 number of multiallelic sites: 1
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SN 0 number of multiallelic SNP sites: 1
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# TSTV, transitions/transversions:
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# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
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TSTV 0 3 5 0.60 3 4 0.75
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# SiS, Singleton stats:
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# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
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SiS 0 1 8 3 5 3 0 0 3
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# AF, Stats by non-reference allele frequency:
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# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
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AF 0 0.000000 8 3 5 3 0 0 3
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# QUAL, Stats by quality:
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# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
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QUAL 0 998 7 3 4 3
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# IDD, InDel distribution:
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# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
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IDD 0 -2 1 0 .
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IDD 0 3 1 0 .
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IDD 0 8 1 0 .
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# ST, Substitution types:
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# ST [2]id [3]type [4]count
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ST 0 A>C 1
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ST 0 A>G 0
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ST 0 A>T 0
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ST 0 C>A 2
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ST 0 C>G 0
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ST 0 C>T 1
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ST 0 G>A 1
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ST 0 G>C 0
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ST 0 G>T 0
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ST 0 T>A 2
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ST 0 T>C 1
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ST 0 T>G 0
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# DP, Depth distribution
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# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
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@ -36,8 +36,8 @@ 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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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: VCF file
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@ -46,7 +46,7 @@ input:
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type: file
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description: tabix index file
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pattern: "*.{tbi}"
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- fasta:
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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@ -43,6 +43,6 @@
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- path: output/bcftools/test.vcf.gz
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md5sum: eb75ae1f08a1884f8edc59ed423471a2
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- path: output/bcftools/test.vcf.gz.tbi
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md5sum: 06d52177f819730dd409157914534e8d
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md5sum: 06d52177f819730dd409157914534e8d
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- path: output/bcftools/test.fa
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md5sum: c9e7ac4537756a0b33bcf17117f9a065
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