def test_simple(self):
file = "/Users/franklinmichael/source/janis/janis/examples/echo.py"
engine = Toil("simple-test")
env = Environment("toil-local", engine, LocalFileScheme())
fromjanis(
file,
env=env,
# dryrun=True,
hints=None,
validation_reqs=None,
)
def test_whole_genome_germline_pmac(self):
file = "/Users/franklinmichael/janis-search-path/wg-germline-30x-pmac.py"
print(
fromjanis(
file,
validation_reqs=ValidationRequirements(
truthVCF=
"/researchers/jiaan.yu/WGS_pipeline/germline/GIAB_NA12878/high_conf_calls/normalised_files/high_conf.norm.vcf",
intervals=
"/researchers/jiaan.yu/WGS_pipeline/germline/GIAB_NA12878/test_cases/test2_WGS_30X/other_files/WGS_30X.bed",
reference=
"/bioinf_core/Proj/hg38_testing/Resources/Gatk_Resource_Bundle_hg38/hg38_contigs_renamed/Homo_sapiens_assembly38.fasta",
fields=[
"variants_gatk",
"variants_vardict",
"variants_strelka",
"combinedVariants",
],
),
env="pmac",
hints={CaptureType.key(): CaptureType.THIRTYX},
dryrun=True,
# inputs="/Users/franklinmichael/janis-search-path/wgs-30x-additional-inputs.json",
watch=False,
))
def test_somatic(self):
file = "/Users/franklinmichael/source/janis-examplepipelines/workflows/somatic_pipeline.py"
fromjanis(
file,
validation_reqs=None,
# validation_reqs=ValidationRequirements(
# truthVCF="/researchers/jiaan.yu/WGS_pipeline/germline/GIAB_NA12878/high_conf_calls/normalised_files/high_conf.norm.vcf",
# intervals="/researchers/jiaan.yu/WGS_pipeline/germline/GIAB_NA12878/test_cases/test2_WGS_30X/other_files/WGS_30X.bed",
# reference="/bioinf_core/Proj/hg38_testing/Resources/Gatk_Resource_Bundle_hg38/hg38_contigs_renamed/Homo_sapiens_assembly38.fasta",
# fields=["variants_gatk", "variants_vardict", "variants_strelka", "combinedVariants"]
# ),
env="local-connect",
hints={CaptureType.key(): CaptureType.TARGETED},
# dryrun=True,
# inputs="wgs-30x-additional-inputs.json"
)
def test_whole_genome_germline_gcp(self):
file = "/Users/franklinmichael/janis-search-path/wg-germline-30x-gcp.py"
print(
fromjanis(
file,
validation_reqs=ValidationRequirements(
truthVCF="gs://peter-mac-cromwell/reference/gold.vcf",
intervals="gs://peter-mac-cromwell/reference/WGS_30X.bed",
reference=
"gs://peter-mac-cromwell/reference/assembly_contigs_renamed/Homo_sapiens_assembly38.fasta",
fields=["variants_gatk"],
),
env="gcp",
hints={CaptureType.key(): CaptureType.THIRTYX},
dryrun=True,
inputs=
"/Users/franklinmichael/janis-search-path/wgs-30x-additional-inputs.json",
watch=False,
))
def do_run(args):
jc = JanisConfiguration.initial_configuration(args.config)
validation_reqs, batchrun_reqs = None, None
if args.validation_fields:
Logger.info("Will prepare validation")
validation_reqs = ValidationRequirements(
truthVCF=args.validation_truth_vcf,
reference=args.validation_reference,
fields=args.validation_fields,
intervals=args.validation_intervals,
)
if args.batchrun:
Logger.info("Will prepare batch run")
batchrun_reqs = BatchRunRequirements(fields=args.batchrun_fields,
groupby=args.batchrun_groupby)
hints = {
k[5:]: v
for k, v in vars(args).items()
if k.startswith("hint_") and v is not None
}
# the args.extra_inputs parameter are inputs that we MUST match
# we'll need to parse them manually and then pass them to fromjanis as requiring a match
required_inputs = parse_additional_arguments(args.extra_inputs)
inputs = args.inputs or []
# we'll manually suck "inputs" out of the extra parms, otherwise it's actually really
# annoying if you forget to put the inputs before the workflow positional argument.
# TBH, we could automatically do this for all params, but it's a little trickier
if "inputs" in required_inputs:
ins = required_inputs.pop("inputs")
inputs.extend(ins if isinstance(ins, list) else [ins])
if "i" in required_inputs:
ins = required_inputs.pop("i")
inputs.extend(ins if isinstance(ins, list) else [ins])
keep_intermediate_files = args.keep_intermediate_files is True
db_config = jc.cromwell.get_database_config_helper()
if args.mysql:
db_config.should_manage_mysql = True
if args.no_database:
db_config.skip_database = True
if args.development:
# no change for using mysql, as a database is the default
keep_intermediate_files = True
JanisConfiguration.manager().cromwell.call_caching_enabled = True
wid = fromjanis(
args.workflow,
name=args.name,
validation_reqs=validation_reqs,
batchrun_reqs=batchrun_reqs,
engine=args.engine,
filescheme=args.filescheme,
hints=hints,
output_dir=args.output_dir,
inputs=inputs,
required_inputs=required_inputs,
filescheme_ssh_binding=args.filescheme_ssh_binding,
cromwell_url=args.cromwell_url,
watch=args.progress,
max_cores=args.max_cores,
max_mem=args.max_memory,
force=args.no_cache,
recipes=args.recipe,
keep_intermediate_files=keep_intermediate_files,
run_in_background=(args.background is True),
run_in_foreground=(args.foreground is True),
dbconfig=db_config,
only_toolbox=args.toolbox,
no_store=args.no_store,
allow_empty_container=args.allow_empty_container,
check_files=not args.skip_file_check,
container_override=parse_container_override_format(
args.container_override),
)
Logger.info("Exiting")
raise SystemExit