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…rganization.csv file into the raw data folder.
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Hello @emanuega! Thanks for updating this PR.
Comment last updated at 2020-11-24 02:48:31 UTC |
Codecov Report
@@ Coverage Diff @@
## v0.1.7 #66 +/- ##
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- Coverage 87.33% 68.67% -18.66%
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Files 57 57
Lines 5108 5140 +32
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- Hits 4461 3530 -931
- Misses 647 1610 +963
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… parameter sets when these are randomly selected and save into the parameters since these saved parameters will no longer match the specified parameters.
seichhorn
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seichhorn
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Looks good, couple points I was hoping you could address
| stored in the dataSet, overwriting any previously stored | ||
| DataOrganization. | ||
| The DataOrganization is located in the following search order: | ||
| i) If filePath is specified and filePath exists this file is copied |
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Could you change this to indicate to the user that it first looks for the filepath, if it doesn't find that it falls back to looking for the filepath prepended with merlin.DATA_ORGANIZATION_HOME. It also seems like we should issue a warning or error to the user if they have something in filepath that doesn't exist in either location, in case it is able to get a dataorganiation file from one of the other two if statements.
| print('Running MERlin pipeline through snakemake') | ||
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| if 'restart_times' not in snakemakeParameters: | ||
| snakemakeParameters['restart_times'] = 3 |
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I worry that the typical user would not expect this behavior and might not understand why they have one job restarting itself. Could we log this somewhere the user might expect to find this type of information?
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| def __init__(self, dataSet, filePath: str = None): | ||
| def __init__(self, dataSet, filePath: str = None, | ||
| dataPortal: dataportal.DataPortal = None): |
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Should there be a way to add a dataportal when constructing an analysis folder with merlin.py?
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Allow raw images to be placed in a "Data" subdirectory and allow a data organization file to be included in the raw data directory. Allow the report path to specified and submit no report if no path is specified.