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Adding meta to multivcfanalyzer, updating test to nf-test (#5773)
* Adding meta to multivcfanalyzer, updating test to nf-test * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * fix meta.yml * Add sort to vcfs * Add tab to tags * add checks for files due to failing md5 sums across docker,conda,singularity --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| nextflow_process { | ||
|
|
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| name "Test Process MULTIVCFANALYZER" | ||
| script "../main.nf" | ||
| process "MULTIVCFANALYZER" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "multivcfanalyzer" | ||
| tag "gunzip" | ||
| tag "gatk/unifiedgenotyper" | ||
|
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| setup { | ||
| run("GATK_UNIFIEDGENOTYPER") { | ||
| script "../../gatk/unifiedgenotyper/main.nf" | ||
| process{ | ||
| """ | ||
| input[0] = Channel.of([ [ id:'test' ], // meta map | ||
| file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), | ||
| file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) | ||
| ], | ||
| [ [ id:'test2' ], // meta map | ||
| file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true), | ||
| file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) | ||
| ] | ||
| ) | ||
| input[1] = [ [], | ||
| file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) | ||
| ] | ||
| input[2] = [ [], | ||
| file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) | ||
| ] | ||
| input[3] = [ [], | ||
| file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) | ||
| ] | ||
| input[4] = [[],[]] | ||
| input[5] = [[],[]] | ||
| input[6] = [[],[]] | ||
| input[7] = [[],[]] | ||
| """ | ||
| } | ||
| } | ||
| run("GUNZIP") { | ||
| script "../../gunzip/main.nf" | ||
| process{ | ||
| """ | ||
| input[0] = GATK_UNIFIEDGENOTYPER.out.vcf | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
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| test("sarscov2 - vcf") { | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]} | ||
| input[1] = [ [] , | ||
| file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) | ||
| ] | ||
| input[2] = [[],[]] | ||
| input[3] = [[],[]] | ||
| input[4] = true | ||
| input[5] = 30 | ||
| input[6] = 5 | ||
| input[7] = 0.8 | ||
| input[8] = 0.2 | ||
| input[9] = [[],[]] | ||
| """ | ||
| } | ||
| } | ||
|
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||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.snptable_snpeff, | ||
| process.out.json, | ||
| process.out.versions, | ||
| file(process.out.info_txt[0][1]).readLines().any { it.contains('Run finished:') }, | ||
| file(process.out.full_alignment[0][1]).readLines().any { it.contains('>') }, | ||
| file(process.out.snp_alignment[0][1]).readLines().any { it.contains('>') }, | ||
| file(process.out.snp_genome_alignment[0][1]).readLines().any { it.contains('>Reference') }, | ||
| file(process.out.snpstatistics[0][1]).readLines().any { it.contains('SNP statistics for') }, | ||
| file(process.out.snptable[0][1]).readLines().any { it.contains('Position') }, | ||
| file(process.out.snptable_uncertainty[0][1]).readLines().any { it.contains('Position') }, | ||
| file(process.out.structure_genotypes[0][1]).readLines().any { it.contains('-1') }, | ||
| file(process.out.structure_genotypes_nomissing[0][1]).readLines().any { it.contains('-1') }).match() | ||
| } | ||
| ) | ||
| } | ||
|
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| } | ||
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| test("sarscov2 - vcf - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]} | ||
| input[1] = [ [] , | ||
| file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) | ||
| ] | ||
| input[2] = [[],[]] | ||
| input[3] = [[],[]] | ||
| input[4] = true | ||
| input[5] = 30 | ||
| input[6] = 5 | ||
| input[7] = 0.8 | ||
| input[8] = 0.2 | ||
| input[9] = [[],[]] | ||
| """ | ||
| } | ||
| } | ||
|
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
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||
| } | ||
|
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||
| } |
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