diff --git a/software/bcftools/consensus/main.nf b/software/bcftools/consensus/main.nf index 794b854e..2a15136c 100644 --- a/software/bcftools/consensus/main.nf +++ b/software/bcftools/consensus/main.nf @@ -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 """ diff --git a/tests/data/README.md b/tests/data/README.md index 6e94c988..8d02d790 100644 --- a/tests/data/README.md +++ b/tests/data/README.md @@ -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 ` ### generic diff --git a/tests/data/dummy/dummy_file2.txt b/tests/data/dummy/dummy_file2.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/data/generic/vcf/test.consensus.fa b/tests/data/generic/vcf/test.consensus.fa deleted file mode 100644 index d7688b04..00000000 --- a/tests/data/generic/vcf/test.consensus.fa +++ /dev/null @@ -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 diff --git a/tests/data/generic/vcf/test.vcf b/tests/data/generic/vcf/test.vcf deleted file mode 100644 index 88895fc7..00000000 --- a/tests/data/generic/vcf/test.vcf +++ /dev/null @@ -1,24 +0,0 @@ -##fileformat=VCFv4.2 -##FORMAT= -##reference=file://some/path/human_g1k_v37.fasta -##INFO= -##INFO= -##ALT= -##contig= -##contig= -#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 . 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 diff --git a/tests/data/generic/vcf/test.vcf.gz b/tests/data/generic/vcf/test.vcf.gz deleted file mode 100644 index da39e1d1..00000000 Binary files a/tests/data/generic/vcf/test.vcf.gz and /dev/null differ diff --git a/tests/data/generic/vcf/test.vcf.gz.tbi b/tests/data/generic/vcf/test.vcf.gz.tbi deleted file mode 100644 index eafa4b88..00000000 Binary files a/tests/data/generic/vcf/test.vcf.gz.tbi and /dev/null differ diff --git a/tests/data/generic/vcf/test2.vcf.gz b/tests/data/generic/vcf/test2.vcf.gz deleted file mode 100644 index da39e1d1..00000000 Binary files a/tests/data/generic/vcf/test2.vcf.gz and /dev/null differ diff --git a/tests/data/generic/vcf/test2.vcf.gz.tbi b/tests/data/generic/vcf/test2.vcf.gz.tbi deleted file mode 100644 index eafa4b88..00000000 Binary files a/tests/data/generic/vcf/test2.vcf.gz.tbi and /dev/null differ diff --git a/tests/data/generic/vcf/test3.vcf.gz b/tests/data/generic/vcf/test3.vcf.gz deleted file mode 100644 index da39e1d1..00000000 Binary files a/tests/data/generic/vcf/test3.vcf.gz and /dev/null differ diff --git a/tests/data/generic/vcf/test3.vcf.gz.tbi b/tests/data/generic/vcf/test3.vcf.gz.tbi deleted file mode 100644 index eafa4b88..00000000 Binary files a/tests/data/generic/vcf/test3.vcf.gz.tbi and /dev/null differ diff --git a/tests/data/generic/vcf/test_a.merge.vcf.gz b/tests/data/generic/vcf/test_a.merge.vcf.gz deleted file mode 100644 index 7ab659d7..00000000 Binary files a/tests/data/generic/vcf/test_a.merge.vcf.gz and /dev/null differ diff --git a/tests/data/generic/vcf/test_a.merge.vcf.gz.tbi b/tests/data/generic/vcf/test_a.merge.vcf.gz.tbi deleted file mode 100644 index 9ce37bf9..00000000 Binary files a/tests/data/generic/vcf/test_a.merge.vcf.gz.tbi and /dev/null differ diff --git a/tests/data/generic/vcf/test_b.merge.vcf.gz b/tests/data/generic/vcf/test_b.merge.vcf.gz deleted file mode 100644 index 751f5a66..00000000 Binary files a/tests/data/generic/vcf/test_b.merge.vcf.gz and /dev/null differ diff --git a/tests/data/generic/vcf/test_b.merge.vcf.gz.tbi b/tests/data/generic/vcf/test_b.merge.vcf.gz.tbi deleted file mode 100644 index eadd6a4d..00000000 Binary files a/tests/data/generic/vcf/test_b.merge.vcf.gz.tbi and /dev/null differ diff --git a/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam new file mode 100644 index 00000000..e86eb955 Binary files /dev/null and b/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam differ diff --git a/tests/data/genomics/sarscov2/vcf/test.vcf b/tests/data/genomics/sarscov2/vcf/test.vcf new file mode 100644 index 00000000..02a8a1f6 --- /dev/null +++ b/tests/data/genomics/sarscov2/vcf/test.vcf @@ -0,0 +1,41 @@ +##fileformat=VCFv4.2 +##FILTER= +##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= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_callVersion=1.11+htslib-1.11 +##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 10:55:13 2021 +##FILTER=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 diff --git a/tests/data/genomics/sarscov2/vcf/test.vcf.gz b/tests/data/genomics/sarscov2/vcf/test.vcf.gz new file mode 100644 index 00000000..96257004 Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test.vcf.gz differ diff --git a/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi b/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi new file mode 100644 index 00000000..f6e862ed Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test.vcf.gz.tbi differ diff --git a/tests/data/genomics/sarscov2/vcf/test2.vcf b/tests/data/genomics/sarscov2/vcf/test2.vcf new file mode 100644 index 00000000..02a8a1f6 --- /dev/null +++ b/tests/data/genomics/sarscov2/vcf/test2.vcf @@ -0,0 +1,41 @@ +##fileformat=VCFv4.2 +##FILTER= +##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= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_callVersion=1.11+htslib-1.11 +##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 10:55:13 2021 +##FILTER=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 diff --git a/tests/data/genomics/sarscov2/vcf/test2.vcf.gz b/tests/data/genomics/sarscov2/vcf/test2.vcf.gz new file mode 100644 index 00000000..96257004 Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test2.vcf.gz differ diff --git a/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi b/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi new file mode 100644 index 00000000..f6e862ed Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi differ diff --git a/tests/data/genomics/sarscov2/vcf/test3.vcf b/tests/data/genomics/sarscov2/vcf/test3.vcf new file mode 100644 index 00000000..a62ed968 --- /dev/null +++ b/tests/data/genomics/sarscov2/vcf/test3.vcf @@ -0,0 +1,42 @@ +##fileformat=VCFv4.2 +##FILTER= +##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= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##bcftools_callVersion=1.11+htslib-1.11 +##bcftools_callCommand=call -Ou -mv; Date=Mon Mar 8 13:13:34 2021 +##FILTER=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 diff --git a/tests/data/genomics/sarscov2/vcf/test3.vcf.gz b/tests/data/genomics/sarscov2/vcf/test3.vcf.gz new file mode 100644 index 00000000..21e819de Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test3.vcf.gz differ diff --git a/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi b/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi new file mode 100644 index 00000000..d793eb1b Binary files /dev/null and b/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi differ diff --git a/tests/software/bcftools/consensus/main.nf b/tests/software/bcftools/consensus/main.nf index 8b9ce4fe..325de143 100644 --- a/tests/software/bcftools/consensus/main.nf +++ b/tests/software/bcftools/consensus/main.nf @@ -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("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ] ] BCFTOOLS_CONSENSUS ( input ) } diff --git a/tests/software/bcftools/consensus/test.yml b/tests/software/bcftools/consensus/test.yml index 26384b3e..9d239bc2 100644 --- a/tests/software/bcftools/consensus/test.yml +++ b/tests/software/bcftools/consensus/test.yml @@ -5,4 +5,4 @@ - bcftools_consensus files: - path: output/bcftools/test.fa - md5sum: c9e7ac4537756a0b33bcf17117f9a065 + md5sum: e57d3e4d113f989bc069c5fd61627091 diff --git a/tests/software/bcftools/filter/main.nf b/tests/software/bcftools/filter/main.nf index bdf21a59..5ca7e47a 100644 --- a/tests/software/bcftools/filter/main.nf +++ b/tests/software/bcftools/filter/main.nf @@ -6,10 +6,9 @@ nextflow.enable.dsl = 2 include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] ) workflow test_bcftools_filter { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]] + [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]] BCFTOOLS_FILTER ( input ) } diff --git a/tests/software/bcftools/filter/test.yml b/tests/software/bcftools/filter/test.yml index a47d3cd5..b1dfdfba 100644 --- a/tests/software/bcftools/filter/test.yml +++ b/tests/software/bcftools/filter/test.yml @@ -5,4 +5,4 @@ - bcftools_filter files: - path: output/bcftools/test.vcf.gz - md5sum: 16947ce72a127938d881113a1e6e696b + md5sum: 9d491cfa84067450342ba8e66c75e5b8 diff --git a/tests/software/bcftools/isec/main.nf b/tests/software/bcftools/isec/main.nf index 7d22f437..ab214019 100644 --- a/tests/software/bcftools/isec/main.nf +++ b/tests/software/bcftools/isec/main.nf @@ -5,16 +5,13 @@ nextflow.enable.dsl = 2 include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] ) workflow test_bcftools_isec { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${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("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf.gz.tbi", checkIfExists: true)] + ] BCFTOOLS_ISEC ( input ) - } diff --git a/tests/software/bcftools/isec/test.yml b/tests/software/bcftools/isec/test.yml index 8955521e..9fe06207 100644 --- a/tests/software/bcftools/isec/test.yml +++ b/tests/software/bcftools/isec/test.yml @@ -5,18 +5,14 @@ - bcftools_isec files: - path: output/bcftools/test/0000.vcf.gz - md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d + md5sum: fc178eb342a91dc0d1d568601ad8f8e2 - path: output/bcftools/test/0000.vcf.gz.tbi - md5sum: 8484b151ef902e25e54f7713d46ed90e + md5sum: 36e11bf96ed0af4a92caa91a68612d64 - path: output/bcftools/test/0001.vcf.gz - md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d + md5sum: fc178eb342a91dc0d1d568601ad8f8e2 - path: output/bcftools/test/0001.vcf.gz.tbi - md5sum: 8484b151ef902e25e54f7713d46ed90e - - path: output/bcftools/test/0002.vcf.gz - md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d - - path: output/bcftools/test/0002.vcf.gz.tbi - md5sum: 8484b151ef902e25e54f7713d46ed90e + md5sum: 36e11bf96ed0af4a92caa91a68612d64 - path: output/bcftools/test/README.txt - md5sum: 63ef64134d2685bc5d50332ef20389d2 + md5sum: 10fc33b66522645600d44afbd41fb792 - path: output/bcftools/test/sites.txt - md5sum: 01bb949ed7825ecf692bf0640e363647 + md5sum: 1cea3fbde7f6d3c97f3d39036f9690df diff --git a/tests/software/bcftools/merge/main.nf b/tests/software/bcftools/merge/main.nf index d9fe395d..a466e387 100644 --- a/tests/software/bcftools/merge/main.nf +++ b/tests/software/bcftools/merge/main.nf @@ -6,13 +6,12 @@ nextflow.enable.dsl = 2 include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] ) workflow test_bcftools_merge { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${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("${launchDir}/tests/data/genomics/sarscov2/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]] BCFTOOLS_MERGE ( input ) } diff --git a/tests/software/bcftools/merge/test.yml b/tests/software/bcftools/merge/test.yml index 471ea52b..d31ed1b9 100644 --- a/tests/software/bcftools/merge/test.yml +++ b/tests/software/bcftools/merge/test.yml @@ -5,4 +5,4 @@ - bcftools_merge files: - path: output/bcftools/test.vcf.gz - md5sum: 23eee1acfd99581889be3fd2b86b6950 + md5sum: 52165fc4149c61547e63800b876c9661 diff --git a/tests/software/bcftools/mpileup/main.nf b/tests/software/bcftools/mpileup/main.nf index 1c28df55..fed52804 100644 --- a/tests/software/bcftools/mpileup/main.nf +++ b/tests/software/bcftools/mpileup/main.nf @@ -6,12 +6,10 @@ include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf 'args3': '--no-version' ] ) workflow test_bcftools_mpileup { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${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("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ] BCFTOOLS_MPILEUP ( input, fasta ) - } diff --git a/tests/software/bcftools/mpileup/test.yml b/tests/software/bcftools/mpileup/test.yml index 0c55f614..3703286a 100644 --- a/tests/software/bcftools/mpileup/test.yml +++ b/tests/software/bcftools/mpileup/test.yml @@ -5,9 +5,8 @@ - bcftools_mpileup files: - path: output/bcftools/test.vcf.gz - md5sum: f25141161cb935ef7719cfb41563ffb0 + md5sum: 518f770a9d04004c4493fc2167280653 - path: output/bcftools/test.vcf.gz.tbi - md5sum: 4423be9f13fa07e5eadb13b1cbe8baf7 + md5sum: f4be4d707434b3b960fde100b7ec3bf3 - path: output/bcftools/test.bcftools_stats.txt - md5sum: b8d6b6927f7bf024acf11ba438b54fa0 - + md5sum: 2d506e32837a53a01fea0fc90402632a diff --git a/tests/software/bcftools/stats/main.nf b/tests/software/bcftools/stats/main.nf index ee7833da..829e3ca8 100644 --- a/tests/software/bcftools/stats/main.nf +++ b/tests/software/bcftools/stats/main.nf @@ -5,10 +5,9 @@ nextflow.enable.dsl = 2 include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] ) workflow test_bcftools_stats { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]] + [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]] BCFTOOLS_STATS ( input ) } diff --git a/tests/software/bcftools/stats/test.yml b/tests/software/bcftools/stats/test.yml index fdab4904..fa097efc 100644 --- a/tests/software/bcftools/stats/test.yml +++ b/tests/software/bcftools/stats/test.yml @@ -5,4 +5,4 @@ - bcftools_stats files: - path: output/bcftools/test.bcftools_stats.txt - md5sum: abfc6a90f84e24b2cc7e92cbce06200a + md5sum: c4c5938add12a20050eec3782c8ad623 diff --git a/tests/software/gatk4/mergevcfs/main.nf b/tests/software/gatk4/mergevcfs/main.nf index 48b9b15e..49763ae5 100644 --- a/tests/software/gatk4/mergevcfs/main.nf +++ b/tests/software/gatk4/mergevcfs/main.nf @@ -5,27 +5,23 @@ nextflow.enable.dsl = 2 include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] ) workflow test_gatk4_mergevcfs { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${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("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ] - ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true) + ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true) GATK4_MERGEVCFS ( input, ref_dict, true ) } diff --git a/tests/software/gatk4/mergevcfs/test.yml b/tests/software/gatk4/mergevcfs/test.yml index 4f053cc1..2bd2e50c 100644 --- a/tests/software/gatk4/mergevcfs/test.yml +++ b/tests/software/gatk4/mergevcfs/test.yml @@ -5,7 +5,7 @@ - gatk4_mergevcfs files: - path: output/gatk4/test.merged.vcf.gz - md5sum: f25850b7bd4d362b5ea67d4453e9df55 + md5sum: ff48f175e26db2d4b2957762f6d1c715 - name: gatk4 mergevcfs refdict command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config @@ -14,4 +14,4 @@ - gatk4_mergevcfs files: - path: output/gatk4/test.merged.vcf.gz - md5sum: f25850b7bd4d362b5ea67d4453e9df55 + md5sum: ff48f175e26db2d4b2957762f6d1c715 diff --git a/tests/software/tabix/bgzip/main.nf b/tests/software/tabix/bgzip/main.nf index 9e32e24a..7042a283 100644 --- a/tests/software/tabix/bgzip/main.nf +++ b/tests/software/tabix/bgzip/main.nf @@ -5,10 +5,9 @@ nextflow.enable.dsl = 2 include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] ) workflow test_tabix_bgzip { - def input = [] input = [ [ id:'test' ], // meta map - [ file("${launchDir}/tests/data/generic/vcf/test.vcf", checkIfExists: true) ]] + [ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]] TABIX_BGZIP ( input ) } diff --git a/tests/software/tabix/bgzip/test.yml b/tests/software/tabix/bgzip/test.yml index d75918e9..7e284124 100644 --- a/tests/software/tabix/bgzip/test.yml +++ b/tests/software/tabix/bgzip/test.yml @@ -5,4 +5,4 @@ - tabix_bgzip files: - path: ./output/tabix/test.vcf.gz - md5sum: 40419fb7562475d1c8ec4ab725796de2 + md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d diff --git a/tests/software/tabix/tabix/main.nf b/tests/software/tabix/tabix/main.nf index d89f6aee..45aa9b4d 100644 --- a/tests/software/tabix/tabix/main.nf +++ b/tests/software/tabix/tabix/main.nf @@ -25,7 +25,7 @@ workflow test_tabix_tabix_gff { workflow test_tabix_tabix_vcf { def input = [] input = [ [ id:'test.vcf' ], // meta map - [ file("${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 ) } diff --git a/tests/software/tabix/tabix/test.yml b/tests/software/tabix/tabix/test.yml index 288ef78c..6ee3bbb8 100644 --- a/tests/software/tabix/tabix/test.yml +++ b/tests/software/tabix/tabix/test.yml @@ -24,4 +24,4 @@ - vcf files: - path: output/tabix/test.vcf.gz.tbi - md5sum: a03f56d3e968f32256ffb9f6b7d01812 + md5sum: bbec39fd53cf2834909d52094980d094