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f4c69bc427
* bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
22 lines
519 B
Text
22 lines
519 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
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process STUB_BCLCONVERT_INPUT {
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output:
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path "SampleSheet.csv" ,emit: samplesheet
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path "DDMMYY_SERIAL_FLOWCELL" ,emit: run_dir
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stub:
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"""
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mkdir DDMMYY_SERIAL_FLOWCELL
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echo "SampleSheet" > SampleSheet.csv
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"""
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}
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workflow test_bclconvert {
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STUB_BCLCONVERT_INPUT ()
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BCLCONVERT (STUB_BCLCONVERT_INPUT.out.samplesheet, STUB_BCLCONVERT_INPUT.out.run_dir)
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}
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