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Exchange VCF data by sarscov2 data (#261)

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* 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 2021-03-09 10:04:08 +01:00 committed by GitHub
parent 05cbbbaded
commit a552d97849
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43 changed files with 176 additions and 110 deletions
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12
software/bcftools/consensus/main.nf
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@ -11,19 +11,19 @@ process BCFTOOLS_CONSENSUS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { 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 { } else {
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0" container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
} }
input: input:
tuple val(meta), path(vcf), path(tbi), path(fasta) tuple val(meta), path(vcf), path(tbi), path(fasta)
output: output:
tuple val(meta), path("*.fa"), emit: fasta tuple val(meta), path('*.fa'), emit: fasta
path "*.version.txt" , emit: version path '*.version.txt' , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
@ -31,7 +31,7 @@ process BCFTOOLS_CONSENSUS {
""" """
cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g') 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 echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
""" """

5
tests/data/README.md
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@ -34,6 +34,11 @@ When adding a new module, please check carefully whether the data necessary for
* 'test_genomic.gff3.gz': bgzipped-version * 'test_genomic.gff3.gz': bgzipped-version
* paf * paf
* 'test_cds_from_genomic.paf': PAF file for MT192765.1 genome * '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 ### generic

0
tests/data/dummy/dummy_file2.txt
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20
tests/data/generic/vcf/test.consensus.fa
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@ -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

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tests/data/generic/vcf/test.vcf
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@ -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

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@ -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

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tests/data/genomics/sarscov2/vcf/test2.vcf Normal file
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@ -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

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@ -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

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7
tests/software/bcftools/consensus/main.nf
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@ -5,12 +5,11 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] ) include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
workflow test_bcftools_consensus { workflow test_bcftools_consensus {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ], [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ],
[ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true) ], [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
[ file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ] ] [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ] ]
BCFTOOLS_CONSENSUS ( input ) BCFTOOLS_CONSENSUS ( input )
} }

2
tests/software/bcftools/consensus/test.yml
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@ -5,4 +5,4 @@
- bcftools_consensus - bcftools_consensus
files: files:
- path: output/bcftools/test.fa - path: output/bcftools/test.fa
md5sum: c9e7ac4537756a0b33bcf17117f9a065 md5sum: e57d3e4d113f989bc069c5fd61627091

3
tests/software/bcftools/filter/main.nf
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@ -6,10 +6,9 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] ) include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
workflow test_bcftools_filter { workflow test_bcftools_filter {
def input = [] def input = []
input = [ [ id:'test' ], // meta map 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 ) BCFTOOLS_FILTER ( input )
} }

2
tests/software/bcftools/filter/test.yml
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@ -5,4 +5,4 @@
- bcftools_filter - bcftools_filter
files: files:
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: 16947ce72a127938d881113a1e6e696b md5sum: 9d491cfa84067450342ba8e66c75e5b8

13
tests/software/bcftools/isec/main.nf
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@ -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'] ) include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
workflow test_bcftools_isec { workflow test_bcftools_isec {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true), [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true),
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true), file("${launchDir}/tests/data/genomics/sarscov2/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.gz.tbi", checkIfExists: true),
[ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true), file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.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) ]]
BCFTOOLS_ISEC ( input ) BCFTOOLS_ISEC ( input )
} }

16
tests/software/bcftools/isec/test.yml
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@ -5,18 +5,14 @@
- bcftools_isec - bcftools_isec
files: files:
- path: output/bcftools/test/0000.vcf.gz - path: output/bcftools/test/0000.vcf.gz
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- path: output/bcftools/test/0000.vcf.gz.tbi - path: output/bcftools/test/0000.vcf.gz.tbi
md5sum: 8484b151ef902e25e54f7713d46ed90e md5sum: 36e11bf96ed0af4a92caa91a68612d64
- path: output/bcftools/test/0001.vcf.gz - path: output/bcftools/test/0001.vcf.gz
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- path: output/bcftools/test/0001.vcf.gz.tbi - path: output/bcftools/test/0001.vcf.gz.tbi
md5sum: 8484b151ef902e25e54f7713d46ed90e md5sum: 36e11bf96ed0af4a92caa91a68612d64
- path: output/bcftools/test/0002.vcf.gz
md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
- path: output/bcftools/test/0002.vcf.gz.tbi
md5sum: 8484b151ef902e25e54f7713d46ed90e
- path: output/bcftools/test/README.txt - path: output/bcftools/test/README.txt
md5sum: 63ef64134d2685bc5d50332ef20389d2 md5sum: 10fc33b66522645600d44afbd41fb792
- path: output/bcftools/test/sites.txt - path: output/bcftools/test/sites.txt
md5sum: 01bb949ed7825ecf692bf0640e363647 md5sum: 1cea3fbde7f6d3c97f3d39036f9690df

9
tests/software/bcftools/merge/main.nf
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@ -6,13 +6,12 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] ) include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] )
workflow test_bcftools_merge { workflow test_bcftools_merge {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz", checkIfExists: true), [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz", checkIfExists: true),
file("${launchDir}/tests/data/vcf/test_b.merge.vcf.gz", checkIfExists: true) ], file("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz", checkIfExists: true) ],
[ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz.tbi", checkIfExists: true), [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.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/test3.vcf.gz.tbi", checkIfExists: true) ]]
BCFTOOLS_MERGE ( input ) BCFTOOLS_MERGE ( input )
} }

2
tests/software/bcftools/merge/test.yml
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@ -5,4 +5,4 @@
- bcftools_merge - bcftools_merge
files: files:
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: 23eee1acfd99581889be3fd2b86b6950 md5sum: 52165fc4149c61547e63800b876c9661

6
tests/software/bcftools/mpileup/main.nf
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@ -6,12 +6,10 @@ include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf
'args3': '--no-version' ] ) 'args3': '--no-version' ] )
workflow test_bcftools_mpileup { workflow test_bcftools_mpileup {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]] [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ]]
fasta = [ file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) ] fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
BCFTOOLS_MPILEUP ( input, fasta ) BCFTOOLS_MPILEUP ( input, fasta )
} }

7
tests/software/bcftools/mpileup/test.yml
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@ -5,9 +5,8 @@
- bcftools_mpileup - bcftools_mpileup
files: files:
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: f25141161cb935ef7719cfb41563ffb0 md5sum: 518f770a9d04004c4493fc2167280653
- path: output/bcftools/test.vcf.gz.tbi - path: output/bcftools/test.vcf.gz.tbi
md5sum: 4423be9f13fa07e5eadb13b1cbe8baf7 md5sum: f4be4d707434b3b960fde100b7ec3bf3
- path: output/bcftools/test.bcftools_stats.txt - path: output/bcftools/test.bcftools_stats.txt
md5sum: b8d6b6927f7bf024acf11ba438b54fa0 md5sum: 2d506e32837a53a01fea0fc90402632a

3
tests/software/bcftools/stats/main.nf
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@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] ) include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] )
workflow test_bcftools_stats { workflow test_bcftools_stats {
def input = [] def input = []
input = [ [ id:'test' ], // meta map 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 ) BCFTOOLS_STATS ( input )
} }

2
tests/software/bcftools/stats/test.yml
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@ -5,4 +5,4 @@
- bcftools_stats - bcftools_stats
files: files:
- path: output/bcftools/test.bcftools_stats.txt - path: output/bcftools/test.bcftools_stats.txt
md5sum: abfc6a90f84e24b2cc7e92cbce06200a md5sum: c4c5938add12a20050eec3782c8ad623

16
tests/software/gatk4/mergevcfs/main.nf
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@ -5,27 +5,23 @@ nextflow.enable.dsl = 2
include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] ) include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
workflow test_gatk4_mergevcfs { workflow test_gatk4_mergevcfs {
def input = [] def input = []
input = [ [ id:'test' ], // meta map 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),
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true), file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true) ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
GATK4_MERGEVCFS ( input, ref_dict, false ) GATK4_MERGEVCFS ( input, ref_dict, false )
} }
workflow test_gatk4_mergevcfs_refdict { workflow test_gatk4_mergevcfs_refdict {
def input = [] def input = []
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true), [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true), file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
file("${launchDir}/tests/data/vcf/test3.vcf.gz", 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 ) GATK4_MERGEVCFS ( input, ref_dict, true )
} }

4
tests/software/gatk4/mergevcfs/test.yml
View file

@ -5,7 +5,7 @@
- gatk4_mergevcfs - gatk4_mergevcfs
files: files:
- path: output/gatk4/test.merged.vcf.gz - path: output/gatk4/test.merged.vcf.gz
md5sum: f25850b7bd4d362b5ea67d4453e9df55 md5sum: ff48f175e26db2d4b2957762f6d1c715
- name: gatk4 mergevcfs refdict - name: gatk4 mergevcfs refdict
command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
@ -14,4 +14,4 @@
- gatk4_mergevcfs - gatk4_mergevcfs
files: files:
- path: output/gatk4/test.merged.vcf.gz - path: output/gatk4/test.merged.vcf.gz
md5sum: f25850b7bd4d362b5ea67d4453e9df55 md5sum: ff48f175e26db2d4b2957762f6d1c715

3
tests/software/tabix/bgzip/main.nf
View file

@ -5,10 +5,9 @@ nextflow.enable.dsl = 2
include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] ) include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] )
workflow test_tabix_bgzip { workflow test_tabix_bgzip {
def input = [] def input = []
input = [ [ id:'test' ], // meta map 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 ) TABIX_BGZIP ( input )
} }

2
tests/software/tabix/bgzip/test.yml
View file

@ -5,4 +5,4 @@
- tabix_bgzip - tabix_bgzip
files: files:
- path: ./output/tabix/test.vcf.gz - path: ./output/tabix/test.vcf.gz
md5sum: 40419fb7562475d1c8ec4ab725796de2 md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d

2
tests/software/tabix/tabix/main.nf
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@ -25,7 +25,7 @@ workflow test_tabix_tabix_gff {
workflow test_tabix_tabix_vcf { workflow test_tabix_tabix_vcf {
def input = [] def input = []
input = [ [ id:'test.vcf' ], // meta map 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 ) TABIX_VCF ( input )
} }

2
tests/software/tabix/tabix/test.yml
View file

@ -24,4 +24,4 @@
- vcf - vcf
files: files:
- path: output/tabix/test.vcf.gz.tbi - path: output/tabix/test.vcf.gz.tbi
md5sum: a03f56d3e968f32256ffb9f6b7d01812 md5sum: bbec39fd53cf2834909d52094980d094