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Remove split bam step from gatk calling #107

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Remove split bam step from gatk calling #107

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de29778
Remove split bam step from gatk calling
jiaan-yu Jun 11, 2021
ebb58eb
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jiaan-yu Aug 13, 2021
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11 changes: 2 additions & 9 deletions janis_bioinformatics/tools/variantcallers/gatk/gatkgermline_variants_4_1_3.py
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@@ -1,11 +1,9 @@
import os
from datetime import date

from janis_core.tool.test_classes import TTestCase
from janis_unix.tools import UncompressArchive
from janis_bioinformatics.tools import gatk4, BioinformaticsTool
from janis_bioinformatics.data_types import FastaWithDict, BamBai, VcfTabix, Bed, Vcf
from janis_bioinformatics.tools import BioinformaticsWorkflow
from janis_bioinformatics.tools import gatk4, BioinformaticsWorkflow
from janis_bioinformatics.tools.common import SplitMultiAllele


Expand Down Expand Up @@ -48,15 +46,10 @@ def constructor(self):
self.input("reference", FastaWithDict)
self.input("snps_dbsnp", VcfTabix)

self.step(
"split_bam",
gatk4.Gatk4SplitReads_4_1_3(bam=self.bam, intervals=self.intervals),
)

self.step(
"haplotype_caller",
gatk4.Gatk4HaplotypeCaller_4_1_3(
inputRead=self.split_bam.out,
inputRead=self.bam,
intervals=self.intervals,
reference=self.reference,
dbsnp=self.snps_dbsnp,
Expand Down
36 changes: 5 additions & 31 deletions janis_bioinformatics/tools/variantcallers/gatk/gatksomatic_variants_4_1_3.py
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@@ -1,14 +1,11 @@
import os
from datetime import date

from janis_core import String, Array, WorkflowBuilder
from janis_core import String
from janis_core.tool.test_classes import TTestCase
from janis_unix.tools import UncompressArchive
from janis_bioinformatics.tools import gatk4, BioinformaticsTool
from janis_bioinformatics.data_types import FastaWithDict, BamBai, VcfTabix, Bed, Vcf
from janis_bioinformatics.tools import BioinformaticsWorkflow
from janis_bioinformatics.tools import gatk4, BioinformaticsWorkflow
from janis_bioinformatics.tools.common import SplitMultiAllele
from janis_bioinformatics.tools.htslib import BGZipLatest, TabixLatest
from janis_bioinformatics.tools.vcftools import VcfToolsvcftoolsLatest


Expand Down Expand Up @@ -38,22 +35,12 @@ def constructor(self):
self.input("panel_of_normals", VcfTabix(optional=True))
self.input("output_bam_name", String(optional=True))

# split normal and tumor bam
self.step(
"normal_split_bam",
self.process_subpipeline(bam=self.normal_bam, intervals=self.intervals),
)
self.step(
"tumor_split_bam",
self.process_subpipeline(bam=self.tumor_bam, intervals=self.intervals),
)

# variant calling + learn read orientation model
self.step(
"mutect2",
gatk4.GatkMutect2_4_1_3(
normalBams=[self.normal_split_bam.out],
tumorBams=[self.tumor_split_bam.out],
normalBams=[self.normal_bam],
tumorBams=[self.tumor_bam],
normalSample=self.normal_name,
intervals=self.intervals,
reference=self.reference,
Expand All @@ -74,7 +61,7 @@ def constructor(self):
self.step(
"getpileupsummaries",
gatk4.Gatk4GetPileUpSummariesLatest(
bam=self.tumor_split_bam.out,
bam=self.tumor_bam,
sites=self.gnomad,
intervals=self.intervals,
),
Expand Down Expand Up @@ -119,19 +106,6 @@ def constructor(self):
self.output("out_bam", source=self.mutect2.bam)
self.output("out", source=self.filterpass.out)

@staticmethod
def process_subpipeline(**connections):
w = WorkflowBuilder("split_bam_subpipeline")

w.input("bam", BamBai)
w.input("intervals", Bed(optional=True))
w.step(
"split_bam", gatk4.Gatk4SplitReads_4_1_3(bam=w.bam, intervals=w.intervals)
)
w.output("out", source=w.split_bam.out)

return w(**connections)

def bind_metadata(self):
self.metadata.version = "4.1.3.0"
self.metadata.dateCreated = date(2019, 2, 1)
Expand Down