def test_docker_entrypoint_script_picard(self):
qc_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'33',
'--run-qc',
]
docker_entrypoint(qc_cli_args)
def test_docker_entrypoint_script_fastqc(self):
qc_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'33',
'--target',
join(self.workdir.name, 'idh1-test-sample', 'fastqc.done'),
]
docker_entrypoint(qc_cli_args)
def test_docker_entrypoint_script_reference_target(self):
reference_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'33',
'--target',
join(self.referencedir.name, 'b37decoy.dict'),
]
docker_entrypoint(reference_cli_args)
def test_dna_only_setup(self):
cli_args = [
'--configfile',
self.dna_only_config_tmpfile.name,
'--dry-run',
'--memory',
'15',
'--somatic-variant-calling-only',
]
# run to make sure it doesn't crash
docker_entrypoint(cli_args)
def test_docker_entrypoint_script(self):
cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'32',
'--target',
join(self.workdir.name, 'idh1-test-sample',
'rna_final.bam'), # valid target
]
# run to make sure it doesn't crash
docker_entrypoint(cli_args)
ok_dna_target_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'15',
'--target',
join(self.workdir.name, 'idh1-test-sample', 'mutect.vcf'),
]
docker_entrypoint(ok_dna_target_cli_args)
variant_target_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--somatic-variant-calling-only',
'--memory',
'15',
]
docker_entrypoint(variant_target_cli_args)
germline_variant_cli_args = [
'--configfile',
self.config_tmpfile.name,
'--dry-run',
'--memory',
'15',
'--target',
join(self.workdir.name, 'idh1-test-sample',
'filtered_covered_normal_germline_snps_indels.vcf'),
]
docker_entrypoint(germline_variant_cli_args)
