def outputs(self) -> List[ToolOutput]:
return [
ToolOutput(
"out",
BamBai(),
glob=InputSelector("outputFilename"),
secondaries_present_as={".bai": "^.bai"},
)
]
def inputs(self):
return [
*super(SeqzBam2SeqBase, self).inputs(),
ToolInput(
"normal",
BamBai(),
prefix="--normal",
position=2,
doc="Name of the BAM/pileup file from the reference/normal sample",
),
ToolInput(
"tumour",
BamBai(),
prefix="--tumor", # How do you spell tumour?
position=4,
doc="Name of the BAM/pileup file from the reference/normal sample",
),
ToolInput(
"wiggle_file",
File(),
prefix="-gc",
position=6,
doc="The GC-content wiggle file",
),
ToolInput(
"fasta_reference",
FastaFai(),
prefix="--fasta",
position=8,
doc="The reference FASTA file used to generate the intermediate pileup. Required when input are BAM",
),
ToolInput(
"output_filename",
Filename(extension=".gz"),
prefix="--output",
position=10,
doc="Name of the output file. To use gzip compression name the file ending in .gz. Default STDOUT.",
),
]
def tests(self):
remote_dir = "https://swift.rc.nectar.org.au/v1/AUTH_4df6e734a509497692be237549bbe9af/janis-test-data/bioinformatics/wgsgermline_data"
return [
TTestCase(
name="basic",
input={
"sample_name": "NA12878-BRCA1",
"fastq": [
f"{remote_dir}/NA12878-BRCA1_R1.fastq.gz",
f"{remote_dir}/NA12878-BRCA1_R2.fastq.gz",
],
"reference": f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"cutadapt_qualityCutoff": 15,
"cutadapt_minimumLength": 50,
"bwamem_markShorterSplits": True,
"sortsam_sortOrder": "coordinate",
"sortsam_createIndex": True,
"sortsam_maxRecordsInRam": 5000000,
"sortsam_tmpDir": "./tmp",
"sortsam_validationStringency": "SILENT",
},
output=BamBai.basic_test(
"out",
2826000,
49688,
f"{remote_dir}/NA12878-BRCA1.bam.flagstat",
),
),
TTestCase(
name="minimal",
input={
"sample_name": "NA12878-BRCA1",
"fastq": [
f"{remote_dir}/NA12878-BRCA1_R1.fastq.gz",
f"{remote_dir}/NA12878-BRCA1_R2.fastq.gz",
],
"reference": f"{remote_dir}/Homo_sapiens_assembly38.chr17.fasta",
"cutadapt_qualityCutoff": 15,
"cutadapt_minimumLength": 50,
"bwamem_markShorterSplits": True,
"sortsam_sortOrder": "coordinate",
"sortsam_createIndex": True,
"sortsam_maxRecordsInRam": 5000000,
"sortsam_tmpDir": "./tmp",
"sortsam_validationStringency": "SILENT",
},
output=self.minimal_test(),
),
]
def inputs(self):
return [
*self.additional_inputs,
ToolInput("bam", BamBai(), position=10),
]