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https://github.com/MillironX/nf-core_modules.git
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e971f538a9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file
22 lines
913 B
Text
22 lines
913 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
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include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : '--ASSUME_SORT_ORDER queryname' ] )
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workflow test_picard_markduplicates_sorted_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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PICARD_MARKDUPLICATES ( input )
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}
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workflow test_picard_markduplicates_unsorted_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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PICARD_MARKDUPLICATES_UNSORTED ( input )
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}
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