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0bdd589163
* added module endorspy and test * added endorspy * Fixed spaces and remove unnecessary lines from test * added extra new line to test.yml * added a prefix to to avoid name collision * Update modules/endorspy/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/endorspy/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Apply suggestions from code review * Update modules/endorspy/main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ENDORSPY } from '../../../modules/endorspy/main.nf'
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include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main.nf'
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include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT2 } from '../../../modules/samtools/flagstat/main.nf'
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include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
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include { SAMTOOLS_INDEX } from '../../../modules/samtools/index/main.nf'
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workflow test_endorspy {
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input = [
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[ 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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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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SAMTOOLS_FLAGSTAT ( input )
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SAMTOOLS_VIEW ( input, [] )
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SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
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input2 = SAMTOOLS_VIEW.out.bam
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.mix(SAMTOOLS_INDEX.out.bai)
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.groupTuple(by:0)
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.map{
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def meta = it[0]
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def bam = it[1][0]
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def bai = it[1][1]
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[meta, bam, bai]
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}
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SAMTOOLS_FLAGSTAT2 ( input2 )
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ch_input_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat.join(SAMTOOLS_FLAGSTAT2.out.flagstat)
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ENDORSPY ( ch_input_flagstat )
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}
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