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https://github.com/MillironX/nf-core_modules.git
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de997825de
* chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
28 lines
863 B
Text
28 lines
863 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' addParams( options: [:] )
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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)
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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)
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SRATOOLS_FASTERQDUMP ( input )
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}
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