Wrapper method that writes all configuration files to the pipeline directory
(self, project_root)
| 1410 | return self._render_config("pipeline_graph.html", {"data": dict_viz}) |
| 1411 | |
| 1412 | def write_configs(self, project_root): |
| 1413 | """Wrapper method that writes all configuration files to the pipeline |
| 1414 | directory |
| 1415 | """ |
| 1416 | |
| 1417 | # Write resources config |
| 1418 | with open(join(project_root, "resources.config"), "w") as fh: |
| 1419 | fh.write(self.resources) |
| 1420 | |
| 1421 | # Write containers config |
| 1422 | with open(join(project_root, "containers.config"), "w") as fh: |
| 1423 | fh.write(self.containers) |
| 1424 | |
| 1425 | # Write containers config |
| 1426 | with open(join(project_root, "params.config"), "w") as fh: |
| 1427 | fh.write(self.params) |
| 1428 | |
| 1429 | # Write manifest config |
| 1430 | with open(join(project_root, "manifest.config"), "w") as fh: |
| 1431 | fh.write(self.manifest) |
| 1432 | |
| 1433 | # Write user config if not present in the project directory |
| 1434 | if not exists(join(project_root, "user.config")): |
| 1435 | with open(join(project_root, "user.config"), "w") as fh: |
| 1436 | fh.write(self.user_config) |
| 1437 | |
| 1438 | lib_dir = join(project_root, "lib") |
| 1439 | if not exists(lib_dir): |
| 1440 | os.makedirs(lib_dir) |
| 1441 | with open(join(lib_dir, "Helper.groovy"), "w") as fh: |
| 1442 | fh.write(self.help) |
| 1443 | |
| 1444 | # Generate the pipeline DAG |
| 1445 | pipeline_to_json = self.render_pipeline() |
| 1446 | with open(splitext(self.nf_file)[0] + ".html", "w") as fh: |
| 1447 | fh.write(pipeline_to_json) |
| 1448 | |
| 1449 | def export_params(self): |
| 1450 | """Export pipeline params as a JSON to stdout |