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"