Update artic to v.1.6.0 #6693
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Update artic to v.1.6.0 #6693
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…ith matching primers and model data
- Restructured xml layout to be more pretty and consistent - Tests now working for standard inputs - Added new test for additional params - Added new params such as fuzzy and align_consensus - Rewrote help to be more informative and user friendly
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The linting failure is on a URL which is valid. Is there a way to re-run the tests? |
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Linting fails due to 404: But that URL works? The URL is mentioned in the help section. Edit: just saw your message @pvanheus. I've reran the linting again (had to push a small change). Still the same error. Not sure why its failing on a valid address. |
pvanheus
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Jan 24, 2025
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All checks are passing! @bernt-matthias I have incorporated all your comments. Im unsure about the data table integration, if I have gotten it wrong (sorry!) please let me know. |
| <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> | ||
| <param name="min_quality" type="integer" min="0" value="7" | ||
| label="Eliminate reads with a mean base quality score of less than" | ||
| <param name="max_length" type="integer" value="700" label="Remove reads longer than" help="remove reads greater than this number of base pairs" /> |
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Lab Maximum length would be better IMO.
| <param name="min_quality" type="integer" min="0" value="7" | ||
| label="Eliminate reads with a mean base quality score of less than" | ||
| <param name="max_length" type="integer" value="700" label="Remove reads longer than" help="remove reads greater than this number of base pairs" /> | ||
| <param name="min_length" type="integer" value="400" label="Remove reads shorter than" help="remove reads less than this number of base pairs" /> |
| label="Eliminate reads with a mean base quality score of less than" | ||
| <param name="max_length" type="integer" value="700" label="Remove reads longer than" help="remove reads greater than this number of base pairs" /> | ||
| <param name="min_length" type="integer" value="400" label="Remove reads shorter than" help="remove reads less than this number of base pairs" /> | ||
| <param name="min_quality" |
| @@ -9,4 +9,8 @@ | |||
| <columns>value, dbkey, name, path</columns> | |||
| <file path="${__HERE__}/test-data/all_fasta.loc" /> | |||
| </table> | |||
| <table name="model" comment_char="#"> | |||
| <columns>value, name, platform, path</columns> | |||
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Would a version column be useful here? Or often has in other cases.
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FOR CONTRIBUTOR:
This pull request updates the
articwrapper to the latest version (1.6.0), incorporates the clair3 models data manager and also allows the user to manually specify the model from their history. There is one test that is purposefully commented out, it is to test specifying the model from history. The clair3 models are too big and are restricted, therefore they can not be included in the test-data.Pinging @pvanheus as he is/was working on the clair3 data manager.
There was a minor change to the
gupplyplexwrapper to set the min/max as optional parameters. This makes writing workflows easier with optional inputs with a default value.I have ticked unrestricted checkbox even though it relies on the clair3 tools and the ONT models. The tool itself is MIT licensed.
As always open to any changes!