def requires(self):
if self.matched_n != '':
return [
bam_processing.index_bam(sample=self.case + '_T',
fastq_file=self.tumor,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg),
bam_processing.index_bam(sample=self.case + '_N',
fastq_file=self.matched_n,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg),
msings_baseline(project_dir=self.project_dir,
max_threads=self.max_threads,
case_dict=self.case_dict,
cfg=self.cfg)
]
else:
return [
bam_processing.index_bam(sample=self.case + '_T',
fastq_file=self.tumor,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg),
msings_baseline(project_dir=self.project_dir,
max_threads=self.max_threads,
case_dict=self.case_dict,
cfg=self.cfg)
]
def test_index_bam():
# sort so you can index
output_fp = bp.create_sorted_bam(INPUT_BAM)
bp.index_bam(output_fp)
assert os.path.isfile(INPUT_BAM + '.bai')
def requires(self):
return [
somatic_vcf_intersection(case=self.case,
tumor=self.tumor,
matched_n=self.matched_n,
vcf_path=self.vcf_path,
project_dir=self.project_dir,
max_threads=self.max_threads,
case_dict=self.case_dict,
cfg=self.cfg),
bam_processing.index_bam(sample=self.case + '_T',
fastq_file=self.tumor,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
]
def requires(self):
# if self.matched_n != '':
# return [bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads), bam_processing.index_bam(sample=self.case + '_N', fastq_file=self.matched_n, project_dir=self.project_dir, max_threads=self.max_threads)]
# else:
return bam_processing.index_bam(sample=self.sample,
fastq_file=self.fastq_file,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
def requires(self):
# return bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads)
return [
bam_processing.index_bam(sample=case_name + '_N',
fastq_file=self.case_dict[case_name]['N'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
for case_name in self.case_dict
if self.case_dict[case_name]['N'] != ''
]
def requires(self):
requirements = [
cnvkit_prep(max_threads=self.max_threads,
project_dir=self.project_dir,
cfg=self.cfg,
case_dict=self.case_dict)
]
if self.case_dict[self.case]['N'] != '':
return requirements + [
bam_processing.index_bam(
sample=self.case + '_T',
fastq_file=self.case_dict[self.case]['T'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg),
bam_processing.index_bam(
sample=self.case + '_N',
fastq_file=self.case_dict[self.case]['N'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)]
sample=self.case + '_T',
fastq_file=self.case_dict[self.case]['T'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg),
bam_processing.index_bam(
sample=self.case + '_N',
fastq_file=self.case_dict[self.case]['N'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)]
else:
return requirements + [
bam_processing.index_bam(
sample=self.case + '_T',
fastq_file=self.case_dict[self.case]['T'],
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)]
def output(self):
tumor_out = [
luigi.LocalTarget(
os.path.join(self.project_dir, 'output', 'cnvkit', 'coverage',
'%s_T.targetcoverage.cnn' % self.case)),
luigi.LocalTarget(
os.path.join(self.project_dir, 'output', 'cnvkit', 'coverage',
'%s_T.antitargetcoverage.cnn' % self.case))
]
def requires(self):
return bam_processing.index_bam(sample=self.case + '_T',
fastq_file=self.tumor,
project_dir=self.project_dir,
max_threads=self.max_threads,
cfg=self.cfg)
