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,
))
from ..gatk4toolbase import Gatk4ToolBase
from ... import BioinformaticsTool
CORES_TUPLE = [
# (CaptureType.key(), {
# CaptureType.CHROMOSOME: 2,
# CaptureType.EXOME: 2,
# CaptureType.THIRTYX: 2,
# CaptureType.NINETYX: 2,
# CaptureType.THREEHUNDREDX: 2
# })
]
MEM_TUPLE = [(
CaptureType.key(),
{
CaptureType.TARGETED: 32,
CaptureType.CHROMOSOME: 64,
CaptureType.EXOME: 64,
CaptureType.THIRTYX: 64,
CaptureType.NINETYX: 64,
CaptureType.THREEHUNDREDX: 64,
},
)]
class Gatk4LearnReadOrientationModelBase(Gatk4ToolBase, ABC):
@classmethod
def gatk_command(cls):
return "LearnReadOrientationModel"
