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2e619add87
* created template for `samtools/ampliconclip` (#584) * All tests passing (#584) * Linting fixed (#584) * Final linting fixed (#584) * Optional output flags moved to `input` (#584) * typo fix (#584) * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' addParams([:])
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workflow test_samtools_ampliconclip_no_stats_no_rejects {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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save_cliprejects = false
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save_clipstats = false
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SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
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}
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workflow test_samtools_ampliconclip_no_stats_with_rejects {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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save_cliprejects = true
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save_clipstats = false
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SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
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}
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workflow test_samtools_ampliconclip_with_stats_with_rejects {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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save_cliprejects = true
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save_clipstats = true
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SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
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}
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