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https://github.com/MillironX/nf-core_modules.git
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e080f4c8ac
* fix: remove left-over unnecessary code * Adds support for meta lists for unzip and untar * Fix test inputs * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Fix MALTEXTRACT/AMPS * Fix further modules * Fix cellranger * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
28 lines
879 B
Text
28 lines
879 B
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 )
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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 )
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}
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