def out_bam(self):
# Output is an S3 object
return sl.ContainerTargetInfo(
self,
os.path.join(self.base_s3_folder,
"align_bwa_{}".format(self.ref_name),
"{}.{}.bam".format(self.ref_name, self.sample_name)))
def out_json(self):
# Output is an S3 object
return sl.ContainerTargetInfo(
self,
os.path.join(
self.output_folder,
self.sample_name + ".json.gz"
)
)
def out_file(self):
return sl.ContainerTargetInfo(self, self.path)
def out_summary(self):
return sl.ContainerTargetInfo(self, self.summary_path)
def out_file(self):
# File on S3
return sl.ContainerTargetInfo(
self,
self.s3_url
)
def out_tsv(self):
# Output is an S3 object
return sl.ContainerTargetInfo(
self,
os.path.join(self.base_s3_folder, "virfinder",
self.sample_name + ".tsv"))
def out_json(self):
# JSON summary of all data
return sl.ContainerTargetInfo(
self,
os.path.join(self.output_folder, self.output_prefix + ".json.gz"))
def out_daa(self):
# DIAMOND database
return sl.ContainerTargetInfo(
self, os.path.join(self.output_folder,
self.output_prefix + ".dmnd"))
def out_tsv(self):
# Output is a tarball with all of the results
return sl.ContainerTargetInfo(
self,
os.path.join(self.output_folder, self.sample_name + ".checkm.tsv"))
def out_fastq(self):
# Output is an S3 object
return sl.ContainerTargetInfo(
self,
os.path.join(self.base_s3_folder, "reads",
self.sra_accession + ".fastq.gz"))
