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…lt). If the KEY exists then: - .get(key) will return its value, otherwise None - .get(key, default) will return its value, otherwise default What these methods DON'T do is change based on the VALUE. They don't return None/default if the value is None, '', or otherwise evaluates to False in a boolean context. It seems I've beem assuming the opposite. Embarrassing. Fortunately all of these corrections are for very unlikely cases (things like users deleting expected keys or changing their type, or features with a Parent= tag that is missing a value). The most likely case is when setting the default value for Run Config's `run_name`, which is pretty harmless.
… missing keys in the PathsFile class. Adding this to check_backward_compatibility()
In the Run Config bowtie section: - Comment lines for each key now have the descriptive command line option indicated In the CWL for bowtie: - The names for aligned and unaligned sequence files are now determined within the CommandLineTool CWL which cleans up the Workflow CWL and is consistent with the approach for stdout/stderr file naming - The `logfile` input was removed because it isn't used - The ordering of command line options is now consistent with their order in the bowtie help string
…. The Stage 1 section has been cleaned up a bit. Some sections which were specific to Stage 1 now describe features that are used across the Features Sheet, so this content has been moved to the Features Sheet section in Configuration.md. Selector formats have also been updated in the Stage 3 section.
…nstead of providing another summary of the selection process, I'm instead using this space to focus on the file itself which I think is more appropriate. I've added a table to indicate which selectors support things like wildcards and lists.
…nstead of providing another summary of the selection process, I'm instead using this space to focus on the file itself which I think is more appropriate. I've added a table to indicate which selectors support things like wildcards and lists.
… `run_directory` key is actually for the suffix of the final output directory name, and that it is optional. Also adding a small correction to ensure that subdirectory structure is preserved if it is present in `run_directory`
- GFF files are optional - Workaround solution for experiments with more than one control condition - Normalization constants in Samples Sheet can be used for spike-in normalization
…onfiguration.md, and it is more appropriate there. Removing this sentence for being redundant and having misleading context
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More updates:
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…ather than "Our ___ utilities"
…e modified between runs, and resume runs create their own processed Run Config copies
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More updates:
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A couple minor issues:
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…bust for a wider variety of inputs. The user might omit the value (resulting in None rather than an empty string), or the user might want to use integer values (0 being particularly tricky) for these settings. Both of these cases would previously result in unexpected behavior. Changes to Configuration constructor arguments: - Added skip_setup which minimally loads the Run Config and the settings from Paths File and stops. Useful for testing. - Renamed validate_inputs to validate_gffs. Previous value was misleading; validation of the Paths File and Samples Sheet was still being performed when validate_inputs=False, and we don't have a use case for making the behavior consistent for those files.
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Thanks for catching that, I made those changes too hastily and neglected to test because it seemed so straightforward. I've addressed this bug, wrote some test cases for it, and addressed a couple of other edge cases. Users can provide empty values, empty strings, and integers in
Addressed in b8d51be |
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Documentation:
Workflow:
-mfor providing the drop threshold for reads with too many alignmentsRun Config:
tiny-plot:
class_chartsandrule_chartsBug fixes:
run_namein the Run Config). These bugs would have triggered an exception shortly after so there is no concern about compromised accuracy.