mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
Exchange VCF data by sarscov2 data (#261)
* added sarscov2 vcf data; adjusted bcftools tests * updated README.md * deleted old VCF files; fixed mergevcfs * fixed tabix
This commit is contained in:
Kevin Menden
GitHub
parent
05cbbbaded
commit
a552d97849
43 changed files with 176 additions and 110 deletions
|
|
@ -11,19 +11,19 @@ process BCFTOOLS_CONSENSUS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.11' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container 'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0'
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fa"), emit: fasta
|
||||
path "*.version.txt" , emit: version
|
||||
tuple val(meta), path('*.fa'), emit: fasta
|
||||
path '*.version.txt' , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
|
@ -31,7 +31,7 @@ process BCFTOOLS_CONSENSUS {
|
|||
"""
|
||||
cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
|
||||
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
|
||||
sed -i "s/\${header}/${meta.id}/g" ${prefix}.fa
|
||||
sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
|
||||
|
||||
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -34,6 +34,11 @@ When adding a new module, please check carefully whether the data necessary for
|
|||
* 'test_genomic.gff3.gz': bgzipped-version
|
||||
* paf
|
||||
* 'test_cds_from_genomic.paf': PAF file for MT192765.1 genome
|
||||
* vcf
|
||||
* 'test.vcf', 'test2.vcf': generated from 'test_paired_end.sorted.bam' using bcftools mpileup, call and filter
|
||||
* 'test3.vcf': generated from 'test_single_end.sorted.bam' using bcftools mpileup, call and filter
|
||||
* '*.gz': generated from VCF files using bgzip
|
||||
* '.tbi': generated from '.vcf.gz' files using `tabix -p vcf -f <file>`
|
||||
|
||||
### generic
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +0,0 @@
|
|||
>1:2-501
|
||||
TACcAtATgTgACAtATAAaAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTG
|
||||
cAGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATT
|
||||
AAATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAAT
|
||||
ATTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTC
|
||||
TTGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAAC
|
||||
TTCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAG
|
||||
GTCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTG
|
||||
ATGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATC
|
||||
TTTAAAAACAAAAAAAAAGAA
|
||||
>2
|
||||
gaagatcttttccttattaaggatctgaagctctgtagatttgtattctattaaacatgg
|
||||
AgagattagtgattttccatattctttaagtcattttagagtaatgtgttcttaagatAa
|
||||
atcagaaaaacaaaaacttgtgctttcctgtttgaaaaacaaacagctgtggggaatgGt
|
||||
gtcgggacagcctttttatAaaatttttctaaataatgttgaggctttgatacgtcaaag
|
||||
ttatatttcaaatggaatcacttagacctcgtttctgagtgtcaatggccatattggggA
|
||||
tttgctgctgccaatgacaGcacaccctgggaatgccccaactacttactacaaagcagt
|
||||
gttacatggagaagatcttcaagagtctttttgctagatctttccttggcttttgatgtg
|
||||
actcctctcaataaaatccacagtaatatagtgagtggtctcctgctccaaaccagtatt
|
||||
Tcagacacagttaatccagac
|
||||
|
|
@ -1,24 +0,0 @@
|
|||
##fileformat=VCFv4.2
|
||||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
||||
##reference=file://some/path/human_g1k_v37.fasta
|
||||
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
|
||||
##INFO=<ID=MinDP,Number=1,Type=Integer,Description="Dummy">
|
||||
##ALT=<ID=DEL,Description="Deletion">
|
||||
##contig=<ID=1,assembly=b37,length=249250621>
|
||||
##contig=<ID=2,assembly=b37,length=249250621>
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001
|
||||
1 5 . C A . PASS . GT 0/1
|
||||
1 5 . C T . PASS . GT 0/1
|
||||
1 7 . T A . PASS . GT .
|
||||
1 10 . G A . PASS . GT 0/1
|
||||
1 12 . GACA GA . PASS . GT 0/1
|
||||
1 16 . T TAAA . PASS . GT 1/1
|
||||
1 19 . A C . PASS . GT 0/1
|
||||
1 61 . C A . PASS . GT 0/1
|
||||
2 61 . agag aa . PASS . GT 0/1
|
||||
2 119 . aaa t . PASS . GT 0/1
|
||||
2 179 . g gacgtacgt . PASS . GT 0/1
|
||||
2 200 . a <DEL> . PASS END=210 GT 1/0
|
||||
2 300 . a . . PASS END=310;MinDP=10 GT 0/1
|
||||
2 320 . a <*> . PASS END=330;MinDP=20 GT 0/1
|
||||
2 481 . t c,a . PASS . GT 0/2
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
BIN
tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam
Normal file
BIN
tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam
Normal file
Binary file not shown.
41
tests/data/genomics/sarscov2/vcf/test.vcf
Normal file
41
tests/data/genomics/sarscov2/vcf/test.vcf
Normal file
|
|
@ -0,0 +1,41 @@
|
|||
##fileformat=VCFv4.2
|
||||
##FILTER=<ID=PASS,Description="All filters passed">
|
||||
##bcftoolsVersion=1.11+htslib-1.11
|
||||
##bcftoolsCommand=mpileup -Ou -f data/genomics/sarscov2/fasta/test_genome.fasta data/genomics/sarscov2/bam/test_paired_end.sorted.bam
|
||||
##reference=file://data/genomics/sarscov2/fasta/test_genome.fasta
|
||||
##contig=<ID=MT192765.1,length=29829>
|
||||
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
|
||||
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
|
||||
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
|
||||
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
|
||||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
|
||||
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
|
||||
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
|
||||
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
|
||||
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
|
||||
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
|
||||
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
|
||||
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
|
||||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
|
||||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
||||
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
|
||||
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
|
||||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
|
||||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
||||
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
|
||||
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
|
||||
##bcftools_callVersion=1.11+htslib-1.11
|
||||
##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 10:55:13 2021
|
||||
##FILTER=<ID=LowQual,Description="Set if true: %QUAL<1 || DP>0">
|
||||
##bcftools_filterVersion=1.11+htslib-1.11
|
||||
##bcftools_filterCommand=filter -s LowQual -e '%QUAL<1 || DP>0'; Date=Mon Mar 8 10:55:13 2021
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT data/genomics/sarscov2/bam/test_paired_end.sorted.bam
|
||||
MT192765.1 197 . G T 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 4788 . C T 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 8236 . C A 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 10506 . TTATGACTGTGTCTCTTTTTGTTACATGCACCATATG TTATG 18.4617 LowQual INDEL;IDV=1;IMF=0.333333;DP=3;VDB=0.5;SGB=-0.379885;MQSB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,1,1,0;MQ=60 GT:PL 0/1:51,0,54
|
||||
MT192765.1 11037 . T C 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 15009 . G A 30.4183 LowQual DP=2;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:60,3,0
|
||||
MT192765.1 18807 . T C 136 LowQual DP=6;VDB=0.618918;SGB=-0.590765;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,4;MQ=60 GT:PL 1/1:166,15,0
|
||||
MT192765.1 23813 . T C 4.38466 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:32,3,0
|
||||
MT192765.1 24103 . A G 30.4183 LowQual DP=2;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:60,3,0
|
||||
BIN
tests/data/genomics/sarscov2/vcf/test.vcf.gz
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test.vcf.gz
Normal file
Binary file not shown.
BIN
tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi
Normal file
Binary file not shown.
41
tests/data/genomics/sarscov2/vcf/test2.vcf
Normal file
41
tests/data/genomics/sarscov2/vcf/test2.vcf
Normal file
|
|
@ -0,0 +1,41 @@
|
|||
##fileformat=VCFv4.2
|
||||
##FILTER=<ID=PASS,Description="All filters passed">
|
||||
##bcftoolsVersion=1.11+htslib-1.11
|
||||
##bcftoolsCommand=mpileup -Ou -f data/genomics/sarscov2/fasta/test_genome.fasta data/genomics/sarscov2/bam/test_paired_end.sorted.bam
|
||||
##reference=file://data/genomics/sarscov2/fasta/test_genome.fasta
|
||||
##contig=<ID=MT192765.1,length=29829>
|
||||
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
|
||||
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
|
||||
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
|
||||
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
|
||||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
|
||||
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
|
||||
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
|
||||
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
|
||||
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
|
||||
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
|
||||
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
|
||||
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
|
||||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
|
||||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
||||
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
|
||||
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
|
||||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
|
||||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
||||
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
|
||||
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
|
||||
##bcftools_callVersion=1.11+htslib-1.11
|
||||
##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 10:55:13 2021
|
||||
##FILTER=<ID=LowQual,Description="Set if true: %QUAL<1 || DP>0">
|
||||
##bcftools_filterVersion=1.11+htslib-1.11
|
||||
##bcftools_filterCommand=filter -s LowQual -e '%QUAL<1 || DP>0'; Date=Mon Mar 8 10:55:13 2021
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT data/genomics/sarscov2/bam/test_paired_end.sorted.bam
|
||||
MT192765.1 197 . G T 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 4788 . C T 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 8236 . C A 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 10506 . TTATGACTGTGTCTCTTTTTGTTACATGCACCATATG TTATG 18.4617 LowQual INDEL;IDV=1;IMF=0.333333;DP=3;VDB=0.5;SGB=-0.379885;MQSB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,1,1,0;MQ=60 GT:PL 0/1:51,0,54
|
||||
MT192765.1 11037 . T C 7.30814 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 15009 . G A 30.4183 LowQual DP=2;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:60,3,0
|
||||
MT192765.1 18807 . T C 136 LowQual DP=6;VDB=0.618918;SGB=-0.590765;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,4;MQ=60 GT:PL 1/1:166,15,0
|
||||
MT192765.1 23813 . T C 4.38466 LowQual DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:32,3,0
|
||||
MT192765.1 24103 . A G 30.4183 LowQual DP=2;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:60,3,0
|
||||
BIN
tests/data/genomics/sarscov2/vcf/test2.vcf.gz
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test2.vcf.gz
Normal file
Binary file not shown.
BIN
tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi
Normal file
Binary file not shown.
42
tests/data/genomics/sarscov2/vcf/test3.vcf
Normal file
42
tests/data/genomics/sarscov2/vcf/test3.vcf
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
##fileformat=VCFv4.2
|
||||
##FILTER=<ID=PASS,Description="All filters passed">
|
||||
##bcftoolsVersion=1.11+htslib-1.11
|
||||
##bcftoolsCommand=mpileup -Ou -f ../fasta/test_genome.fasta ../bam/test_single_end.sorted.bam
|
||||
##reference=file://../fasta/test_genome.fasta
|
||||
##contig=<ID=MT192765.1,length=29829>
|
||||
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
|
||||
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
|
||||
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
|
||||
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
|
||||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
|
||||
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
|
||||
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
|
||||
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
|
||||
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
|
||||
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
|
||||
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
|
||||
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
|
||||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
|
||||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
|
||||
##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
|
||||
##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
|
||||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
|
||||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
|
||||
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
|
||||
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
|
||||
##bcftools_callVersion=1.11+htslib-1.11
|
||||
##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 13:13:34 2021
|
||||
##FILTER=<ID=LowQual,Description="Set if true: %QUAL<1 || DP>1">
|
||||
##bcftools_filterVersion=1.11+htslib-1.11
|
||||
##bcftools_filterCommand=filter -s LowQual -e '%QUAL<1 || DP>1'; Date=Mon Mar 8 13:13:34 2021
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ../bam/test_single_end.sorted.bam
|
||||
MT192765.1 3744 . A T 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=36 GT:PL 1/1:36,3,0
|
||||
MT192765.1 4788 . C T 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 8236 . C A 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 10506 . TTATGACTGTGTCTCTTTTTGTTACATGCACCATATG TTATG 21.4353 LowQual INDEL;IDV=1;IMF=0.5;DP=2;VDB=0.78;SGB=-0.379885;MQSB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,1,0;MQ=60 GT:PL 0/1:54,0,54
|
||||
MT192765.1 11037 . T C 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 15009 . G A 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 15636 . AG A 8.99861 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 1/1:38,3,0
|
||||
MT192765.1 18807 . T C 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
MT192765.1 18820 . TCC TC 6.51141 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:35,3,0
|
||||
MT192765.1 24103 . A G 7.30814 PASS DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60 GT:PL 1/1:36,3,0
|
||||
BIN
tests/data/genomics/sarscov2/vcf/test3.vcf.gz
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test3.vcf.gz
Normal file
Binary file not shown.
BIN
tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi
Normal file
BIN
tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi
Normal file
Binary file not shown.
|
|
@ -5,12 +5,11 @@ nextflow.enable.dsl = 2
|
|||
include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_bcftools_consensus {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ] ]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ] ]
|
||||
|
||||
BCFTOOLS_CONSENSUS ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools_consensus
|
||||
files:
|
||||
- path: output/bcftools/test.fa
|
||||
md5sum: c9e7ac4537756a0b33bcf17117f9a065
|
||||
md5sum: e57d3e4d113f989bc069c5fd61627091
|
||||
|
|
|
|||
|
|
@ -6,10 +6,9 @@ nextflow.enable.dsl = 2
|
|||
include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
|
||||
|
||||
workflow test_bcftools_filter {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]]
|
||||
|
||||
BCFTOOLS_FILTER ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools_filter
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
md5sum: 16947ce72a127938d881113a1e6e696b
|
||||
md5sum: 9d491cfa84067450342ba8e66c75e5b8
|
||||
|
|
|
|||
|
|
@ -5,16 +5,13 @@ nextflow.enable.dsl = 2
|
|||
include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
|
||||
|
||||
workflow test_bcftools_isec {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)],
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test2.vcf.gz.tbi", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz", checkIfExists: true)],
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi", checkIfExists: true)]
|
||||
]
|
||||
|
||||
BCFTOOLS_ISEC ( input )
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,18 +5,14 @@
|
|||
- bcftools_isec
|
||||
files:
|
||||
- path: output/bcftools/test/0000.vcf.gz
|
||||
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
- path: output/bcftools/test/0000.vcf.gz.tbi
|
||||
md5sum: 8484b151ef902e25e54f7713d46ed90e
|
||||
md5sum: 36e11bf96ed0af4a92caa91a68612d64
|
||||
- path: output/bcftools/test/0001.vcf.gz
|
||||
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
- path: output/bcftools/test/0001.vcf.gz.tbi
|
||||
md5sum: 8484b151ef902e25e54f7713d46ed90e
|
||||
- path: output/bcftools/test/0002.vcf.gz
|
||||
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
|
||||
- path: output/bcftools/test/0002.vcf.gz.tbi
|
||||
md5sum: 8484b151ef902e25e54f7713d46ed90e
|
||||
md5sum: 36e11bf96ed0af4a92caa91a68612d64
|
||||
- path: output/bcftools/test/README.txt
|
||||
md5sum: 63ef64134d2685bc5d50332ef20389d2
|
||||
md5sum: 10fc33b66522645600d44afbd41fb792
|
||||
- path: output/bcftools/test/sites.txt
|
||||
md5sum: 01bb949ed7825ecf692bf0640e363647
|
||||
md5sum: 1cea3fbde7f6d3c97f3d39036f9690df
|
||||
|
|
|
|||
|
|
@ -6,13 +6,12 @@ nextflow.enable.dsl = 2
|
|||
include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] )
|
||||
|
||||
workflow test_bcftools_merge {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test_b.merge.vcf.gz", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz.tbi", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test_b.merge.vcf.gz.tbi", checkIfExists: true) ]]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz", checkIfExists: true) ],
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]]
|
||||
|
||||
BCFTOOLS_MERGE ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools_merge
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
md5sum: 23eee1acfd99581889be3fd2b86b6950
|
||||
md5sum: 52165fc4149c61547e63800b876c9661
|
||||
|
|
|
|||
|
|
@ -6,12 +6,10 @@ include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf
|
|||
'args3': '--no-version' ] )
|
||||
|
||||
workflow test_bcftools_mpileup {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]]
|
||||
fasta = [ file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) ]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ]]
|
||||
fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
|
||||
|
||||
BCFTOOLS_MPILEUP ( input, fasta )
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,9 +5,8 @@
|
|||
- bcftools_mpileup
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
md5sum: f25141161cb935ef7719cfb41563ffb0
|
||||
md5sum: 518f770a9d04004c4493fc2167280653
|
||||
- path: output/bcftools/test.vcf.gz.tbi
|
||||
md5sum: 4423be9f13fa07e5eadb13b1cbe8baf7
|
||||
md5sum: f4be4d707434b3b960fde100b7ec3bf3
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
md5sum: b8d6b6927f7bf024acf11ba438b54fa0
|
||||
|
||||
md5sum: 2d506e32837a53a01fea0fc90402632a
|
||||
|
|
|
|||
|
|
@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
|
|||
include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_bcftools_stats {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]]
|
||||
|
||||
BCFTOOLS_STATS ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools_stats
|
||||
files:
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
md5sum: abfc6a90f84e24b2cc7e92cbce06200a
|
||||
md5sum: c4c5938add12a20050eec3782c8ad623
|
||||
|
|
|
|||
|
|
@ -5,27 +5,23 @@ nextflow.enable.dsl = 2
|
|||
include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_gatk4_mergevcfs {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
|
||||
|
||||
ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
|
||||
ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
|
||||
|
||||
GATK4_MERGEVCFS ( input, ref_dict, false )
|
||||
}
|
||||
|
||||
workflow test_gatk4_mergevcfs_refdict {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
|
||||
|
||||
ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
|
||||
ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
|
||||
|
||||
GATK4_MERGEVCFS ( input, ref_dict, true )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4_mergevcfs
|
||||
files:
|
||||
- path: output/gatk4/test.merged.vcf.gz
|
||||
md5sum: f25850b7bd4d362b5ea67d4453e9df55
|
||||
md5sum: ff48f175e26db2d4b2957762f6d1c715
|
||||
|
||||
- name: gatk4 mergevcfs refdict
|
||||
command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
|
||||
|
|
@ -14,4 +14,4 @@
|
|||
- gatk4_mergevcfs
|
||||
files:
|
||||
- path: output/gatk4/test.merged.vcf.gz
|
||||
md5sum: f25850b7bd4d362b5ea67d4453e9df55
|
||||
md5sum: ff48f175e26db2d4b2957762f6d1c715
|
||||
|
|
|
|||
|
|
@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
|
|||
include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_tabix_bgzip {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/vcf/test.vcf", checkIfExists: true) ]]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]]
|
||||
|
||||
TABIX_BGZIP ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- tabix_bgzip
|
||||
files:
|
||||
- path: ./output/tabix/test.vcf.gz
|
||||
md5sum: 40419fb7562475d1c8ec4ab725796de2
|
||||
md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ workflow test_tabix_tabix_gff {
|
|||
workflow test_tabix_tabix_vcf {
|
||||
def input = []
|
||||
input = [ [ id:'test.vcf' ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/vcf/test.vcf.gz", checkIfExists: true) ] ]
|
||||
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ] ]
|
||||
|
||||
TABIX_VCF ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,4 +24,4 @@
|
|||
- vcf
|
||||
files:
|
||||
- path: output/tabix/test.vcf.gz.tbi
|
||||
md5sum: a03f56d3e968f32256ffb9f6b7d01812
|
||||
md5sum: bbec39fd53cf2834909d52094980d094
|
||||
|
|
|
|||
Loading…
Reference in a new issue