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Implement new auto-process 'info' command #895

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merged 7 commits into from
Dec 20, 2023
+143 −3
Merged

Implement new auto-process 'info' command #895

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79d1237
auto_process.py: initial implementation of new 'info' command.
pjbriggs Oct 20, 2023
a9f975b
Add 'info' command to the command reference documentation.
pjbriggs Oct 20, 2023
63e240d
'info' command: add bases mask & flow cell mode, and trap for bad dir…
pjbriggs Dec 19, 2023
9e040dd
bcl2fastq/utils: new function 'get_run_config' reports configuration …
pjbriggs Dec 19, 2023
8d0ff9d
metadata: add 'run_configuration' item to 'AnalysisDirMetadata' class.
pjbriggs Dec 19, 2023
04be518
'setup' command: also acquire and store 'run_configuration' metadata …
pjbriggs Dec 19, 2023
449f36f
'info' command: update to add run configuration information.
pjbriggs Dec 19, 2023
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'info' command: update to add run configuration information.
@pjbriggs
pjbriggs committed Dec 20, 2023
commit 449f36f381f3e0298fb4edcf5ca2da00bd7ea404
11 changes: 6 additions & 5 deletions auto_process_ngs/cli/auto_process.py
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Original file line number Diff line number Diff line change
@@ -1300,11 +1300,12 @@ def info(args):
logger.fatal("Missing metadata and/or parameters")
sys.exit(1)
# Report information
print("Run ID : %s" % d.run_id)
print("Platform : %s" % d.metadata.platform)
print("Flow cell mode: %s" % d.metadata.flow_cell_mode)
print("Bases mask : %s" % d.metadata.default_bases_mask)
print("Sample sheet : %s" % d.params.sample_sheet)
print("Run ID : %s" % d.run_id)
print("Platform : %s" % d.metadata.platform)
print("Flow cell mode : %s" % d.metadata.flow_cell_mode)
print("Run configuration : %s" % d.metadata.run_configuration)
print("Default bases mask: %s" % d.metadata.default_bases_mask)
print("Sample sheet : %s" % d.params.sample_sheet)

def metadata(args):
"""