Sha256: 3ef6e58b52a15cb16197456f0531621d61f0ad98fbe76b9f6d2ef448f6f64515
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Versions: 88
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Contents
require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
require 'rbbt/hpc/batch'
require 'rbbt/workflow'
Workflow.require_workflow "Sample"
Workflow.require_workflow "HTS"
class TestSLURM < Test::Unit::TestCase
def _test_batch_options
job = Sample.job(:mutect2, "small", :reference => "hg38")
TmpFile.with_file do |batch_dir|
options = HPC::BATCH.batch_options(job, :batch_dir => batch_dir, :batch_modules => 'java')
iii options
end
end
def _test_template
job = Sample.job(:mutect2, "small", :reference => "hg38")
TmpFile.with_file do |batch_dir|
template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java')
ppp template
end
end
def _test_template_singularity
job = Sample.job(:mutect2, "small", :reference => "hg38")
TmpFile.with_file do |batch_dir|
template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :singularity => true)
ppp template
end
end
def _test_template_contain
job = Sample.job(:mutect2, "small", :reference => "hg38")
TmpFile.with_file do |batch_dir|
template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :contain_and_sync => true, :wipe_container => 'force')
ppp template
end
end
def test_template_singularity_contain
job = Sample.job(:mutect2, "small", :reference => "hg38")
TmpFile.with_file do |batch_dir|
template = HPC::BATCH.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java', :contain_and_sync => true, :wipe_container => 'force', :singularity => true)
ppp template
end
end
end
Version data entries
88 entries across 88 versions & 1 rubygems