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"))