mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
66 lines
2.4 KiB
Text
66 lines
2.4 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
|
include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf'
|
|
|
|
workflow test_sratools_fasterqdump_single_end_with_input {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.settings_file)
|
|
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
|
|
|
|
archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
|
|
UNTAR ( archive )
|
|
|
|
def input = Channel.of([ id:'test_single_end', single_end:true ])
|
|
.combine(UNTAR.out.untar.map{ it[1] })
|
|
|
|
SRATOOLS_FASTERQDUMP(input, settings)
|
|
}
|
|
|
|
workflow test_sratools_fasterqdump_paired_end_with_input {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.settings_file)
|
|
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
|
|
|
|
archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
|
|
UNTAR ( archive )
|
|
|
|
def input = Channel.of([ id:'test_paired_end', single_end:false ])
|
|
.combine(UNTAR.out.untar.map{ it[1] })
|
|
|
|
SRATOOLS_FASTERQDUMP(input, settings)
|
|
}
|
|
|
|
workflow test_sratools_fasterqdump_single_end_without_input {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.settings_file)
|
|
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
|
|
|
|
archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
|
|
UNTAR ( archive )
|
|
|
|
def input = Channel.of([ id:'test_single_end', single_end:true ])
|
|
.combine(UNTAR.out.untar.map{ it[1] })
|
|
|
|
SRATOOLS_FASTERQDUMP(input, file('EXISTS'))
|
|
}
|
|
|
|
workflow test_sratools_fasterqdump_paired_end_without_input {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.settings_file)
|
|
settings.text = "/LIBS/GUID = \"5b0d4b7d-88c7-4802-98fd-e3afd06feb32\"\n/libs/cloud/report_instance_identity = \"true\"\n"
|
|
|
|
archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
|
|
UNTAR ( archive )
|
|
|
|
def input = Channel.of([ id:'test_paired_end', single_end:false ])
|
|
.combine(UNTAR.out.untar.map{ it[1] })
|
|
|
|
SRATOOLS_FASTERQDUMP(input, file('EXISTS'))
|
|
}
|