def check_options(self):
Workflow.check_options(self)
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"logfile": self.logfile,
"via": self.opts.via}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {"job_or_dict": self.job,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path',''),
"logfile": self.logfile,
"via": self.opts.via}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {"job": self.job,
"gl": self.globals,
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job_or_dict": self.job,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path', ''),
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job": self.job,
"gl": self.globals,
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
def check_options(self):
Workflow.check_options(self)
self.suffix = ['merged']
primers_dict = self.sysmod.loadPrimers(os.path.join(self.opts.wdir,'primers.fa'))
self.main_args = {"job": self.job,
"primers_dict": primers_dict,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path',''),
"logfile": self.logfile,
"via": self.opts.via}
return True
def check_options(self):
more_defs = {'discard_pcr_duplicates': (False,),
'find_junctions': (False,),
'stranded': (False,)}
Workflow.check_options(self, more_defs)
self.main_args = {"job": self.job,
"pileup_level": self.opts.pileup_level.split(','),
"via": self.opts.via,
"junctions": self.job.options['find_junctions'] or self.opts.junctions,
"stranded": self.job.options['stranded'] and not self.opts.stranded,
"logfile": self.logfile,
"debugfile": self.debugfile}
return True
def check_options(self):
_mbw = str(self.job.options.get('compute_densities_snp','1')).lower()
more_defs = {'bowtie2': (True,),
'make_bigwigs': (True,_mbw in ['1','true','t'])}
Workflow.check_options(self, more_defs)
mincov = int(self.job.options.get('mincov') or self.opts.mincov)
minsnp = int(self.job.options.get('minsnp') or self.opts.minsnp)
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"mincov": mincov,
"minsnp": minsnp,
"path_to_ref": self.opts.fasta_path,
"via": self.opts.via}
return True
def check_options(self):
Workflow.check_options(self)
self.suffix = ['merged']
primers_dict = self.sysmod.loadPrimers(
os.path.join(self.opts.wdir, 'primers.fa'))
self.main_args = {
"job": self.job,
"primers_dict": primers_dict,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path', ''),
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self,{'bowtie2': (True,)})
map_args = self.job.options.get('map_args',{})
self.job.options['create_gdv_project'] &= self.job.options['compute_densities']
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
Workflow.check_options(self,{'bowtie2': (True,), 'local_align': (False,)})
map_args = self.job.options.get('map_args',{})
if self.job.options['local_align']:
map_args.setdefault("bwt_args",[])
map_args["bwt_args"] += ["--local"]
self.job.options['create_gdv_project'] &= self.job.options['compute_densities']
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
Workflow.check_options(self, {'bowtie2': (True, )})
map_args = self.job.options.get('map_args', {})
self.job.options['create_gdv_project'] &= self.job.options[
'compute_densities']
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
def check_options(self):
_mbw = str(self.job.options.get('compute_densities_snp', '1')).lower()
more_defs = {
'bowtie2': (True, ),
'make_bigwigs': (True, _mbw in ['1', 'true', 't'])
}
Workflow.check_options(self, more_defs)
mincov = int(self.job.options.get('mincov') or self.opts.mincov)
minsnp = int(self.job.options.get('minsnp') or self.opts.minsnp)
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"mincov": mincov,
"minsnp": minsnp,
"path_to_ref": self.opts.fasta_path,
"via": self.opts.via
}
return True
def check_options(self):
more_defs = {
'discard_pcr_duplicates': (False, ),
'find_junctions': (False, ),
'stranded': (False, )
}
Workflow.check_options(self, more_defs)
self.main_args = {
"job": self.job,
"pileup_level": self.opts.pileup_level.split(','),
"via": self.opts.via,
"junctions": self.job.options['find_junctions']
or self.opts.junctions,
"stranded": self.job.options['stranded']
and not self.opts.stranded,
"logfile": self.logfile,
"debugfile": self.debugfile
}
return True
def check_options(self):
Workflow.check_options(self, {
'bowtie2': (True, ),
'local_align': (False, )
})
map_args = self.job.options.get('map_args', {})
if self.job.options['local_align']:
map_args.setdefault("bwt_args", [])
map_args["bwt_args"] += ["--local"]
self.job.options['create_gdv_project'] &= self.job.options[
'compute_densities']
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
