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bd0fa881f6
* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
71 lines
1.4 KiB
Text
71 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FLYE } from '../../../modules/flye/main.nf'
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workflow test_flye_pacbio_raw {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-raw"
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FLYE ( input, mode )
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}
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workflow test_flye_pacbio_corr {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-corr"
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FLYE ( input, mode )
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}
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workflow test_flye_pacbio_hifi {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--pacbio-hifi"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_raw {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-raw"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_corr {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-corr"
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FLYE ( input, mode )
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}
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workflow test_flye_nano_hq {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
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]
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mode = "--nano-hq"
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FLYE ( input, mode )
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}
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