mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
44 lines
1.6 KiB
Text
44 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/custom/sratoolsncbisettings/main.nf'
|
|
|
|
workflow test_sratoolsncbisettings_with_good_existing {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
|
|
settings.copyTo(params.settings_file)
|
|
|
|
CUSTOM_SRATOOLSNCBISETTINGS()
|
|
}
|
|
|
|
workflow test_sratoolsncbisettings_with_bad_existing {
|
|
|
|
file(params.settings_path).mkdirs()
|
|
def settings = file(params.settings_file)
|
|
settings.text = '''
|
|
## auto-generated configuration file - DO NOT EDIT ##
|
|
|
|
config/default = "false"
|
|
/repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
|
|
/repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
|
|
/repository/user/ad/public/apps/file/volumes/flatAd = "."
|
|
/repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
|
|
/repository/user/ad/public/apps/sra/volumes/sraAd = "."
|
|
/repository/user/ad/public/apps/sraPileup/volumes/ad = "."
|
|
/repository/user/ad/public/apps/sraRealign/volumes/ad = "."
|
|
/repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
|
|
/repository/user/ad/public/root = "."
|
|
/repository/user/default-path = "/root/ncbi"
|
|
'''.stripIndent()
|
|
|
|
CUSTOM_SRATOOLSNCBISETTINGS()
|
|
}
|
|
|
|
workflow test_sratoolsncbisettings_with_nonexisting {
|
|
def settings = file(params.settings_file)
|
|
settings.delete()
|
|
|
|
CUSTOM_SRATOOLSNCBISETTINGS()
|
|
}
|