2022-05-08 13:44:13 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SRATOOLS_NCBISETTINGS } from '../../../../modules/sratools/ncbisettings/main.nf'
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workflow test_sratools_ncbisettings_with_good_existing {
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file(params.settings_path).mkdirs()
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2022-05-11 12:13:50 +00:00
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def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
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settings.copyTo(params.settings_file)
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2022-05-08 13:44:13 +00:00
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SRATOOLS_NCBISETTINGS()
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}
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workflow test_sratools_ncbisettings_with_bad_existing {
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file(params.settings_path).mkdirs()
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def settings = file(params.settings_file)
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settings.text = '''
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## auto-generated configuration file - DO NOT EDIT ##
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config/default = "false"
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/repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
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/repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
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/repository/user/ad/public/apps/file/volumes/flatAd = "."
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/repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
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/repository/user/ad/public/apps/sra/volumes/sraAd = "."
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/repository/user/ad/public/apps/sraPileup/volumes/ad = "."
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/repository/user/ad/public/apps/sraRealign/volumes/ad = "."
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/repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
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/repository/user/ad/public/root = "."
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/repository/user/default-path = "/root/ncbi"
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'''.stripIndent()
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SRATOOLS_NCBISETTINGS()
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}
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workflow test_sratools_ncbisettings_with_nonexisting {
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SRATOOLS_NCBISETTINGS()
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}
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