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28 lines
1 KiB
Text
28 lines
1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../modules/untar/main.nf'
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include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf'
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workflow test_sratools_fasterqdump_single_end {
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archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
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UNTAR ( archive )
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def input = Channel.of([ id:'test_single_end', single_end:true ])
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.combine(UNTAR.out.untar.map{ it[1] })
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SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
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}
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workflow test_sratools_fasterqdump_paired_end {
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archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
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UNTAR ( archive )
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def input = Channel.of([ id:'test_paired_end', single_end:false ])
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.combine(UNTAR.out.untar.map{ it[1] })
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SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
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}
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