def recursively_build_workflow_with_layers(layers):
w = WorkflowBuilder(f"scattered_with_{layers}")
w.input("scatters", int, default=3)
w.input("seed_hash", Optional[str])
w.input("bias", Optional[int])
w.step("generate_random_ints",
GenerateIntegers(numbers_to_generate=w.scatters))
w.step(
"generate_hashes",
CalculateMd5HashOfInt(value=w.generate_random_ints.out),
scatter="value",
)
joined_generate_hashes = JoinOperator(w.generate_hashes.out, ",")
if layers > 0:
innerworkflow = recursively_build_workflow_with_layers(layers - 1)
w.step(
"inner",
innerworkflow(scatters=w.generate_random_ints),
scatter="scatters",
)
joined_inner = JoinOperator(w.inner.out_hash, ",")
post_hash_inp = (j.logical.If(
j.logical.IsDefined(w.seed_hash),
w.seed_hash + joined_inner,
joined_inner,
) + joined_generate_hashes)
else:
post_hash_inp = j.logical.If(
j.logical.IsDefined(w.seed_hash),
w.seed_hash + joined_generate_hashes,
joined_generate_hashes,
)
w.step(
"post_hash",
CalculateMd5Hash(value=post_hash_inp),
)
w.output("out_hash", source=w.post_hash.out)
return w
def inputs(self):
return [
*super().inputs(),
*Gatk4GetPileUpSummariesBase.additional_args,
ToolInput(
"bam",
Array(BamBai()),
prefix="-I",
prefix_applies_to_all_elements=True,
doc="The SAM/BAM/CRAM file containing reads.",
position=0,
),
ToolInput(
"sampleName", String(optional=True), doc="Used for naming purposes"
),
ToolInput(
"sites",
VcfTabix(),
prefix="-V",
doc="sites of common biallelic variants",
),
ToolInput(
"intervals",
Bed(optional=True),
prefix="--intervals",
doc="-L (BASE) One or more genomic intervals over which to operate",
),
ToolInput(
"pileupTableOut",
Filename(
prefix=JoinOperator(
FilterNullOperator(
[
FirstOperator(
[InputSelector("sampleName"), "generated"]
),
# If(
# IsDefined(InputSelector("intervals")),
# InputSelector(
# "intervals", remove_file_extension=True
# ),
# "",
# ),
]
),
".",
),
extension=".txt",
),
position=1,
prefix="-O",
),
ToolInput(
"reference",
FastaWithDict(optional=True),
prefix="-R",
doc="reference to use when decoding CRAMS",
),
]
def arguments(self):
return [
ToolArgument("| testsomatic.R |", position=3, shell_quote=False),
ToolArgument("var2vcf_paired.pl", position=4, shell_quote=False),
ToolArgument(
JoinOperator(
[InputSelector("tumorBam"),
InputSelector("normalBam")], "|"),
prefix="-b",
position=1,
shell_quote=True,
),
ToolArgument(InputSelector("tumorName"),
prefix="-N",
position=1,
shell_quote=True),
ToolArgument(
JoinOperator(
[InputSelector("tumorName"),
InputSelector("normalName")], "|"),
prefix="-N",
position=5,
shell_quote=True,
),
ToolArgument(
InputSelector("alleleFreqThreshold"),
prefix="-f",
position=5,
shell_quote=False,
),
ToolArgument(
InputSelector("alleleFreqThreshold"),
prefix="-f",
position=1,
shell_quote=False,
),
ToolArgument(" | bcftools view -O z",
position=6,
shell_quote=False),
]
def arguments(self):
return [
ToolArgument(
StringFormatter(
"-Xmx{memory}G {compression} {otherargs}",
memory=MemorySelector() * 3 / 4,
compression=If(
IsDefined(InputSelector("compression_level")),
"-Dsamjdk.compress_level=" +
InputSelector("compression_level"),
"",
),
otherargs=JoinOperator(
FirstOperator([InputSelector("javaOptions"), []]),
" "),
),
prefix="--java-options",
position=-1,
)
]
def arguments(self):
return [
# CADD
ToolArgument(
If(
IsDefined(InputSelector("caddReference")),
"--plugin CADD,"
+ JoinOperator(
InputSelector("caddReference").assert_not_null(), ","
),
"",
),
shell_quote=False,
),
# Condel
ToolArgument(
If(
IsDefined(InputSelector("condelConfig")),
"--plugin "
+ StringFormatter(
"Condel,{condelconfig},b",
condelconfig=InputSelector("condelConfig").assert_not_null(),
),
"",
),
shell_quote=False,
),
# dbNSFP
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("dbnspReference")),
IsDefined(InputSelector("dbsnpColumns")),
),
"--plugin "
+ StringFormatter(
"dbNSFP,{ref},{cols}",
ref=InputSelector("dbnspReference").assert_not_null(),
cols=JoinOperator(
InputSelector("dbsnpColumns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
# REVEL
ToolArgument(
If(
IsDefined(InputSelector("revelReference")),
"--plugin "
+ StringFormatter(
"REVEL,{ref}",
ref=InputSelector("revelReference").assert_not_null(),
),
"",
),
shell_quote=False,
),
# CUSTOM 1
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("custom1Reference")),
IsDefined(InputSelector("custom1Columns")),
),
"--custom "
+ StringFormatter(
"{ref},{cols}",
ref=InputSelector("custom1Reference").assert_not_null(),
cols=JoinOperator(
InputSelector("custom1Columns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
# CUSTOM 2
ToolArgument(
If(
AndOperator(
IsDefined(InputSelector("custom2Reference")),
IsDefined(InputSelector("custom2Columns")),
),
"--custom "
+ StringFormatter(
"{ref},{cols}",
ref=InputSelector("custom2Reference").assert_not_null(),
cols=JoinOperator(
InputSelector("custom2Columns").assert_not_null(), ","
),
),
"",
),
shell_quote=False,
),
]