Update to Innuca's recipe modules #191
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…s with the appropriate compressing software. Added new directive with container
…on of the expected species vs schema species Co-authored-by: cimendes <iines.mendes@gmail.com> Co-authored-by: miguelpmachado <mpmachado@fc.ul.pt>
- add sampel id to novel alleles file
…n the 80% threshold.
If expected species parameter not provided, bypasses the species verification control.
Codecov Report
@@ Coverage Diff @@
## dev #191 +/- ##
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- Coverage 43.96% 41.59% -2.38%
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Files 67 69 +2
Lines 6036 6404 +368
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+ Hits 2654 2664 +10
- Misses 3382 3740 +358
Continue to review full report at Codecov.
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set columBar to False in mlst .report.json
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Ok don't get spoked by the number of comments or by the work to do.
In my opinion all nf / fc workings are fit to the purpose but the python templates are too sketchy and shady. There are a lot of coding patterns that are not scalable, easy to understand nor clear what it does. Improving documentation is a must, but I also recommend re-thinking the code regarding these string parsers with so many nested if statements. I have left you some suggestions but there is a lot going on that is simply impossible for me to understand without trial/error debugging the code.
Nice effort though when putting these scripts in script templates rather than running them directly from the shell. 💯
| pass_qc = True | ||
| logger.warning("Found a Yersinia scheme ({scheme_mlst}), but it is different from what it was" | ||
| " expected ({scheme})".format(scheme_mlst=scheme_mlst, scheme=scheme)) | ||
| else: |
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This if/elif/else is ok because you have to check for several different conditions
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However, these conditions lack proper explanation of the rational.
Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
Co-Authored-By: cimendes <cimendes@users.noreply.github.com>
This PR updates the modules in Innuca's recipe to incorporate the latest changes in the INNUca pipeline (https://github.com/B-UMMI/INNUca). Several components where updated and/or reworked including integrity_coverage, mlst, process_assembly and process_assembly_mapping. A new component, named "insert_size" was added. I apologize for the length of the PR. They made me do it! :P
Enjoy the code review.
This change is