def requires(self): if self.pre_process_reads == "yes" and self.read_library_type == "pe": return [ bbduk(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "pe_samples.lst"))) ] ] if self.pre_process_reads == "yes" and self.read_library_type == "se": return [ bbduk(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "se_samples.lst"))) ] ] if self.pre_process_reads == "no" and self.read_library_type == "pe": return [ reformat(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "pe_samples.lst"))) ] ] if self.pre_process_reads == "no" and self.read_library_type == "se": return [ reformat(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "se_samples.lst"))) ] ]
def requires(self): if self.seq_platforms == "pe" and self.pre_process_reads=="yes": return [cleanFastq(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]] if self.seq_platforms == "pe" and self.pre_process_reads=="no": return [reformat(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]] # Paired-end with Mate-pair if self.seq_platforms == "pe-mp" and self.pre_process_reads =="yes": return [ [cleanFastq(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [cleanFastq(seq_platforms="mp",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]] ] if self.seq_platforms == "pe-mp" and self.pre_process_reads =="no": return [ [reformat(seq_platforms="pe",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [reformat(seq_platforms="mp",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]] ]
def requires(self): if self.seq_platform == "pacbio" and self.pre_process_reads == "yes": return [ filtlong(seq_platforms="pac", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pac_samples.lst"))) ] ] if self.seq_platform == "pacbio" and self.pre_process_reads == "no": return [ reformat(seq_platforms="pac", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pac_samples.lst"))) ] ] if self.seq_platform == "nanopore" and self.pre_process_reads == "yes": return [ filtlong(seq_platforms="ont", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "ont_samples.lst"))) ] ] if self.seq_platform == "nanopore" and self.pre_process_reads == "no": return [ reformat(seq_platforms="ont", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "ont_samples.lst"))) ] ]
def requires(self): if (self.pre_process_reads == "yes"): return [bbduk(sampleName=self.sampleName), makeTx2Gene()] if (self.pre_process_reads == "no"): return [reformat(sampleName=self.sampleName), makeTx2Gene()]
def requires(self): if (self.pre_process_reads == "yes"): return [ bbduk(sampleName=self.sampleName, read_library_type=self.read_library_type), makeTx2Gene(annotation_file_type=self.annotation_file_type) ] if (self.pre_process_reads == "no"): return [ reformat(sampleName=self.sampleName, read_library_type=self.read_library_type), makeTx2Gene(annotation_file_type=self.annotation_file_type) ]
def requires(self): if self.pre_process_reads == "yes": return [ cleanFastq(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ] if self.pre_process_reads == "no": return [ reformat(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ]
def requires(self): if self.seq_platforms == "pe" and self.pre_process_reads == "yes": return [ [ cleanFastq(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_cleanFastq( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], ] if self.seq_platforms == "pe" and self.pre_process_reads == "no": return [ [ reformat(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_reformat( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], ] if self.seq_platforms == "pe-mp" and self.pre_process_reads == "yes": return [[ cleanFastq(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_cleanFastq( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ cleanFastq(seq_platforms="mp", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "mp_samples.lst"))) ] ]] if self.seq_platforms == "pe-mp" and self.pre_process_reads == "no": return [[ reformat(seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_reformat( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ reformat(seq_platforms="mp", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "mp_samples.lst"))) ] ]] if self.seq_platforms == "pe-pac" and self.pre_process_reads == "yes": return [ [ cleanFastq( seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_cleanFastq( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ filtlong(seq_platforms="pac", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pac_samples.lst"))) ] ] ] if self.seq_platforms == "pe-pac" and self.pre_process_reads == "no": return [ [ reformat( seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_reformat( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ reformat(seq_platforms="pac", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pac_samples.lst"))) ] ] ] if self.seq_platforms == "pe-ont" and self.pre_process_reads == "yes": return [ [ cleanFastq( seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_cleanFastq( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ filtlong(platform="pac", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "ont_samples.lst"))) ] ] ] if self.seq_platforms == "pe-ont" and self.pre_process_reads == "no": return [ [ reformat( seq_platforms="pe", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "pe_samples.lst"))) ] ], [ kmergenie_formater_reformat( os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")) ], [ reformat(seq_platforms="ont", sampleName=i) for i in [ line.strip() for line in open((os.path.join( os.getcwd(), "sample_list", "ont_samples.lst"))) ] ] ]
def requires(self): if self.read_library_type == "pe-lr" and self.pre_process_reads=="yes": return [ [bbduk(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [minia_pe_bbduk(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-lr" and self.pre_process_reads=="no": return [ [reformat(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [minia_pe_reformat(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))], [reformat(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="yes": return [ [bbduk(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [bbduk(read_library_type="mp", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]], [minia_pe_mp_bbduk((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")), (os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")) )], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="no": return [ [reformat(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [reformat(read_library_type="mp", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]], [minia_pe_mp_reformat((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")), (os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")) )], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ]