- def makePathMapper(self, reffiles, **kwargs):
+ def makePathMapper(self, reffiles, stagedir, **kwargs):
+ # type: (List[Any], unicode, **Any) -> PathMapper
if self.work_api == "containers":
return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
"/keep/%s",
if self.work_api == "containers":
return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
"/keep/%s",
def job(self, joborder, output_callback, **kwargs):
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
def job(self, joborder, output_callback, **kwargs):
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)
return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)