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QUILT nf-test and bamlist (nf-core#5515)
* Migrate quilt to nf-test and swithc bamlist to auto generation inside the module * Fix tests * Fix test * Fix tests * Add snap * Update license * Add quilt tag * Specify build hash for conda environment * Specify build hash for conda environment * Undo commit * Update nf-test snapshot * Fix config name * Update snapshot * Update meta.yml * Add r-base to environment * Update snapshot generation * Update meta.yml * Update snap * Update snap * Force sorting * Update snapshot
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| Original file line number | Diff line number | Diff line change |
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| // Input data | ||
| def path = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/" | ||
| def bam = "[${path}NA12878.haplotagged.1.0.bam', checkIfExists: true), ${path}NA12878.ont.1.0.bam', checkIfExists: true), ${path}NA12878.illumina.1.0.bam', checkIfExists: true)]" | ||
| def bai = "[${path}NA12878.haplotagged.1.0.bam.bai', checkIfExists: true), ${path}NA12878.ont.1.0.bam.bai', checkIfExists: true),${path}NA12878.illumina.1.0.bam.bai', checkIfExists: true)]" | ||
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| // Input reference data | ||
| def reference_haplotype_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.hap.gz', checkIfExists: true)" | ||
| def reference_legend_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.legend.gz', checkIfExists: true)" | ||
| def genetic_map_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/CEU-chr20-final.b38.txt.gz', checkIfExists: true)" | ||
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| // Parameters | ||
| def chr = "'chr20'" | ||
| def regions_start = "2000001" | ||
| def regions_end = "2100000" | ||
| def ngen = "100" | ||
| def buffer = "10000" | ||
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| // (optional) input truth data | ||
| def posfile = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.posfile.txt', checkIfExists: true)" | ||
| def phasefile = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.phasefile.txt', checkIfExists: true)" | ||
| def posfile_phasefile = "[[ id:'test', chr:'chr20' ], [$posfile], [$phasefile]]" | ||
| def fasta = "[[id:'test'], []]" | ||
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| // Input channel quilt | ||
| def ch_input = "[ id:'test', chr:'chr20' ], $bam, $bai, [$reference_haplotype_file], [$reference_legend_file], $chr, $regions_start, $regions_end, $ngen, $buffer" | ||
| def ch_input_gmap = "[$ch_input, [$genetic_map_file]]" | ||
| def ch_input_nogmap = "[$ch_input, []]" | ||
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| nextflow_process { | ||
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| name "Test Process QUILT" | ||
| script "../main.nf" | ||
| process "QUILT_QUILT" | ||
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "quilt/quilt" | ||
| tag "quilt" | ||
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| test("QUILT") { | ||
| config ("./quilt_default.config") | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = $ch_input_gmap | ||
| input[1] = $posfile_phasefile | ||
| input[2] = $fasta | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("QUILT no optional files") { | ||
| config ("./quilt_default.config") | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = $ch_input_nogmap | ||
| input[1] = [[id: null], [], []] | ||
| input[2] = $fasta | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("QUILT optional output") { | ||
| config ("./quilt_optional.config") | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = $ch_input_gmap | ||
| input[1] = $posfile_phasefile | ||
| input[2] = $fasta | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| def dir = new File(process.out.plots[0][1]) | ||
| def list = [] | ||
| dir.eachFileRecurse { file -> list << file.getName() } | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.vcf + process.out.tbi + | ||
| list.sort() + | ||
| process.out.rdata + process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| test("QUILT no seed") { | ||
| config ("./quilt_noseed.config") | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = $ch_input_gmap | ||
| input[1] = $posfile_phasefile | ||
| input[2] = $fasta | ||
| """ | ||
| } | ||
| } | ||
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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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