def arguments(self):
return [
# ToolArgument("export VarDict=\"/config/binaries/vardict/1.5.1/bin/VarDict\";", position=0, shell_quote=False),
# ToolArgument("", position=0, shell_quote=False),
ToolArgument("| teststrandbias.R |", position=3, shell_quote=False),
ToolArgument("var2vcf_valid.pl", position=4, shell_quote=False),
]
def arguments(self):
return [
ToolArgument("vt decompose -s ", position=0, shell_quote=False),
ToolArgument("| vt normalize -n -q - ",
position=2,
shell_quote=False),
]
def arguments(self):
return [
ToolArgument("bam", prefix="-I", doc="input data format"),
ToolArgument("cram", prefix="-O", doc="output data format"),
ToolArgument(
"-9", doc="compression settings for output cram file (-1=fast,-9=best)"
),
ToolArgument("3.0", prefix="-V", doc="Cram version to output"),
]
def arguments(self):
return [
ToolArgument("mkdir", position=0, shell_quote=False),
ToolArgument(
InputSelector("output_dir"),
position=1,
shell_quote=False,
),
ToolArgument(";", position=2, shell_quote=False),
ToolArgument("cp", position=3, shell_quote=False),
]
def arguments(self):
return [
ToolArgument("vcf-merge", position=0, shell_quote=False),
ToolArgument("| grep '^##' > header.vcf;", position=2, shell_quote=False),
ToolArgument("vcf-concat", position=3, shell_quote=False),
ToolArgument(
"| grep -v '^##' > content.vcf; cat header.vcf content.vcf",
position=5,
shell_quote=False,
),
]
def arguments(self):
return [
ToolArgument("export TMPDIR=/tmp;", position=1, shell_quote=False),
ToolArgument(
StringFormatter(
"/app/Pisces_v{PISCES_VERSION}/Pisces",
PISCES_VERSION=InputSelector("piscesVersion"),
),
position=3,
shell_quote=False,
),
]
def arguments(self):
return [
ToolArgument("export TMPDIR=/tmp;", position=1, shell_quote=False),
ToolArgument("dotnet", position=2, shell_quote=False),
ToolArgument(
StringFormatter(
"/app/Pisces_v{PISCES_VERSION}/VariantQualityRecalibration.dll",
PISCES_VERSION=InputSelector("piscesVersion"),
),
position=3,
shell_quote=False,
),
]
def arguments(self):
return [
ToolArgument(
"--",
position=2,
shell_quote=False,
),
ToolArgument(
">",
position=5,
shell_quote=False,
),
]
def arguments(self):
return [
ToolArgument(
"bcftools filter -e 'STATUS=\"Germline\"' -o - ",
position=0,
shell_quote=False,
),
ToolArgument(
"| bcftools filter -i 'FILTER==\"PASS\"'",
position=2,
shell_quote=False,
),
]
def arguments(self):
return [
ToolArgument(
"-S",
position=2,
doc=
"Ignored for compatibility with previous samtools versions. Previously this option was "
"required if input was in SAM format, but now the correct format is automatically "
"detected by examining the first few characters of input.",
),
ToolArgument("-h",
position=3,
doc="Include the header in the output."),
ToolArgument("-b", position=4, doc="Output in the BAM format."),
]
def arguments(self):
return [
ToolArgument(
StringFormatter(
"-Xmx{memory}G",
memory=MemorySelector() * 3 / 4,
),
position=-3,
shell_quote=False,
),
ToolArgument("-jar /usr/GenomeAnalysisTK.jar",
position=-2,
shell_quote=False),
ToolArgument(f"-T {self.gatk_command()}",
position=-1,
shell_quote=False),
]
def arguments(self):
return [
ToolArgument("configureStrelkaSomaticWorkflow.py", position=0),
ToolArgument(
StringFormatter(";") + InputSelector("rundir") + "/runWorkflow.py",
position=2,
shell_quote=False,
),
ToolArgument(
CpuSelector(None),
prefix="--jobs",
position=3,
shell_quote=False,
doc=" (-j JOBS) number of jobs, must be an integer or 'unlimited' "
"(default: Estimate total cores on this node for local mode, 128 for sge mode)",
),
]
def arguments(self) -> List[ToolArgument]:
return [
ToolArgument("configManta.py", position=0, shell_quote=False),
ToolArgument(
StringFormatter(";") + InputSelector("runDir") + "/runWorkflow.py",
position=2,
shell_quote=False,
),
ToolArgument(
CpuSelector(None),
position=3,
shell_quote=False,
prefix="-j",
doc="(-j) number of jobs, must be an integer or 'unlimited' "
"(default: Estimate total cores on this node for local mode, 128 for sge mode)",
),
]
def arguments(self):
return [
ToolArgument("| testsomatic.R |", position=3, shell_quote=False),
ToolArgument("var2vcf_paired.pl", position=4, shell_quote=False),
ToolArgument(
InputSelector("tumorBam") + "|" + InputSelector("normalBam"),
prefix="-b",
position=1,
shell_quote=True,
),
ToolArgument(
InputSelector("tumorName"), prefix="-N", position=1, shell_quote=True
),
ToolArgument(
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,
),
]
def arguments(self):
return [
ToolArgument("java", position=0, shell_quote=False),
ToolArgument(
StringFormatter("-Xmx{memory}G",
memory=MemorySelector() * 3 / 4),
position=1,
shell_quote=False,
),
ToolArgument(
StringFormatter(
"/app/agent_{AGENT_VERSION}/lib/trimmer.jar",
AGENT_VERSION=InputSelector("agentVersion"),
),
prefix="-jar",
position=2,
shell_quote=False,
),
]
def arguments(self):
return [
# Ensures the output is compressed
ToolArgument(
"z",
prefix="--output-type",
position=1,
doc="(-O) [<b|u|z|v>] b: compressed BCF, u: uncompressed BCF, "
"z: compressed VCF, v: uncompressed VCF [v]",
)
]
def arguments(self):
return [
ToolArgument(
"metrics.txt",
prefix="M=",
separate_value_from_prefix=False,
doc="file containing metrics from duplicate removal",
),
ToolArgument(
"bam",
prefix="inputformat=",
separate_value_from_prefix=False,
doc="input data format",
),
ToolArgument(
"bam",
prefix="outputFormat=",
separate_value_from_prefix=False,
doc="output data format",
),
]
def arguments(self):
return [
ToolArgument("zcat", position=0, shell_quote=False),
ToolArgument("|", position=1, shell_quote=False),
ToolArgument(
"sed 's/ID=AD,Number=./ID=AD,Number=R/' <",
position=2,
shell_quote=False,
),
ToolArgument("|", position=4, shell_quote=False),
ToolArgument("vt decompose -s - -o -",
position=5,
shell_quote=False),
ToolArgument("|", position=6, shell_quote=False),
ToolArgument("vt normalize -n -q - -o -",
position=7,
shell_quote=False),
ToolArgument("|", position=9, shell_quote=False),
ToolArgument("sed 's/ID=AD,Number=./ID=AD,Number=1/'",
position=10,
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 [
ToolArgument(".",
prefix="--output-dir",
doc="path to demultiplexed output")
]
def arguments(self) -> List[ToolArgument]:
return [
ToolArgument(StringFormatter('test:\\t:escaped:\\n:characters"'))
]
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,
),
]
def arguments(self):
return [
ToolArgument("-b", position=4, doc="Output in the BAM format.")
]
def arguments(self):
return [ToolArgument(">", position=101, shell_quote=False)]
def arguments(self) -> Optional[List[ToolArgument]]:
return [ToolArgument("PE", position=0)]
from janis_core import (
CommandToolBuilder,
ToolInput,
ToolOutput,
File,
WildcardSelector,
String,
ToolArgument,
)
ToolWithOptionalWildcardOutput = CommandToolBuilder(
tool="optional_wildcard_output_tool",
version="v0.1.0",
container="ubuntu:latest",
base_command=[],
arguments=[ToolArgument("echo 1 > ", shell_quote=False)],
inputs=[
ToolInput(
"outputFilename", String(optional=True), default="out.csv", position=1
)
],
outputs=[
ToolOutput("out", File(optional=True), selector=WildcardSelector("*.txt"))
],
)
def arguments(self):
return [
# BWA MEM command
ToolArgument("bwa", position=0, shell_quote=False),
ToolArgument("mem", position=1, shell_quote=False),
ToolArgument(
StringFormatter(
"@RG\\tID:{name}\\tSM:{name}\\tLB:{name}\\tPL:{pl}",
name=InputSelector("sampleName"),
pl=InputSelector("platformTechnology"),
),
prefix="-R",
position=3,
doc="Complete read group header line.",
),
ToolArgument(
CpuSelector(),
prefix="-t",
position=3,
shell_quote=False,
doc="Number of threads. (default = 1)",
),
ToolArgument("|", position=6, shell_quote=False),
# Alt Aware Post Processing command
ToolArgument("k8", position=7, shell_quote=False),
ToolArgument("/opt/conda/bin/bwa-postalt.js",
position=7,
shell_quote=False),
# Samtools View command
ToolArgument("|", position=10, shell_quote=False),
ToolArgument("samtools", position=11, shell_quote=False),
ToolArgument("view", position=12, shell_quote=False),
ToolArgument(
InputSelector("reference"),
prefix="-T",
position=13,
shell_quote=False,
),
ToolArgument(
CpuSelector(),
position=13,
prefix="--threads",
doc="(@) Number of additional threads to use [0]",
shell_quote=False,
),
ToolArgument(
"-h",
position=13,
shell_quote=False,
doc="Include header in the output",
),
ToolArgument(
"-b",
position=13,
shell_quote=False,
doc="Output in the BAM format.",
),
]
def arguments(self):
return [
ToolArgument("bwa", position=0, shell_quote=False),
ToolArgument("mem", position=1, shell_quote=False),
ToolArgument("|", position=5, shell_quote=False),
ToolArgument("samtools", position=6, shell_quote=False),
ToolArgument("view", position=7, shell_quote=False),
ToolArgument(InputSelector("reference"),
prefix="-T",
position=8,
shell_quote=False),
ToolArgument(
CpuSelector(),
position=8,
shell_quote=False,
prefix="--threads",
doc="(-@) Number of additional threads to use [0]",
),
ToolArgument(
"-h",
position=8,
shell_quote=False,
doc="Include the header in the output.",
),
ToolArgument("-b",
position=8,
shell_quote=False,
doc="Output in the BAM format."),
ToolArgument(
StringFormatter(
"@RG\\tID:{name}\\tSM:{name}\\tLB:{name}\\tPL:{pl}",
name=InputSelector("sampleName"),
pl=InputSelector("platformTechnology"),
),
prefix="-R",
position=2,
doc=
"Complete read group header line. ’\\t’ can be used in STR and will be converted to a TAB"
"in the output SAM. The read group ID will be attached to every read in the output. "
"An example is ’@RG\\tID:foo\\tSM:bar’. (Default=null) "
"https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups",
),
ToolArgument(
CpuSelector(),
prefix="-t",
position=2,
shell_quote=False,
doc="Number of threads. (default = 1)",
),
]
def arguments(self):
return [ToolArgument("| awk '{print $1}'", position=2, shell_quote=False)]
def arguments(self) -> List[ToolArgument]:
return [ToolArgument(".", "-d")] # CurrentWorkingDirectory()