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b67556e29f
* Add FastK/Merge * Update modules/fastk/merge/main.nf * Update modules/fastk/merge/meta.yml Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
58 lines
2.2 KiB
Text
58 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FASTK_FASTK } from '../../../../modules/fastk/fastk/main.nf'
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include { FASTK_MERGE } from '../../../../modules/fastk/merge/main.nf'
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workflow test_fastk_merge_hist_only {
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input1 = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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input2= [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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FASTK_FASTK ( Channel.of( input1, input2 ) )
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FASTK_MERGE (
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FASTK_FASTK.out.hist.groupTuple()
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.join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
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.join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
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.map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
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)
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}
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workflow test_fastk_merge_all_files {
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input1 = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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input2= [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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FASTK_FASTK ( Channel.of( input1, input2 ) )
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FASTK_MERGE (
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FASTK_FASTK.out.hist.groupTuple()
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.join( FASTK_FASTK.out.ktab.groupTuple(), remainder: true )
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.join( FASTK_FASTK.out.prof.groupTuple(), remainder: true )
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.map { meta, hist, ktab, prof -> [meta, hist, ktab ? ktab.flatten() : [] , prof ? prof.flatten() : [] ] }
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)
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}
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