tiny-count: '--get-templates' argument#259
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taimontgomery merged 9 commits intomasterfrom Dec 14, 2022
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…es.csv. Example configurations have also been removed from the files in the templates directory.
…t. This argument is mutually exclusive with the --paths-file argument. When it is provided, tiny-count simply copies the template files to the current directory and exits (all other arguments are ignored).
Additional improvements to the tiny-count helpstring:
- The --out-prefix argument is now optional. It defaults to "tiny-count_{timestamp}". While it isn't documented, users can also use the "{timestamp}" token in their own prefix which will be evaluated at runtime.
- Default argument values are now indicated at the end of each argument's help string
- A more succinct intro description that doesn't mention tinyRNA's recount/replot option
- The --help and --all-features arguments are now hidden from the helpstring (and the entry for All Features has been removed from Parameters.md)
…me out of date info in the standalone section. Removed the warning about reusing the same prefix between standalone runs since the default prefix solves this issue, and we give users the ability to avoid it themselves with the "{timestamp}" substring. Also moved the selection diagram down so that it is right before the Stage 1 section
…help string so users know they can use it in their own
…ests/testdata/config_files since these files are used in unit tests. All unit tests have been updated to reflect the new config file layout. Updated a few unit tests for collapser and plotter that were out of date.
…ew earlier). I also noticed that there was a tiny-count parameter listed in Parameters.md that is no longer available, so I removed it and audited the rest of Parameters.md making a few small corrections
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Reviewed documentation and did some very minor testing. |
AlexTate
changed the title
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--get-templates
--get-templatescannot be used in combination with the--paths-fileargumentget-templates(sans leading dashes), but this was surprisingly difficult to accomplish without a lot of hacking in argparse, so this was the cleaner and more reliable solutionMisc. improvements to the tiny-count helpstring
--out-prefixargument is now optional. This had to be done to allow a mutually exclusive required group between--get-templatesand--paths-file. Its default value is "tiny-count_{timestamp}". The "{timestamp}" token is replaced with the current date/time. Users can also use this token in their own prefix--helpand--all-featuresarguments are now hidden from the helpstring (and the entry for All Features has been removed from the documentation)Configuration file changes
Input FASTQ Filesheader has been renamed toFASTQ/SAM Filesin the Samples SheetMisc changes
tiny get-templatehas been corrected totiny get-templates(plural)