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Renovate read aggregation EPP and include ONT / AVITI #386

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Renovate read aggregation EPP and include ONT / AVITI #386

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kedhammar
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Suspect at least verification is required.

@kedhammar kedhammar self-assigned this Jan 16, 2025
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Test for Illumina
https://ngi-lims-stage.scilifelab.se/clarity/work-details/1062118

@alneberg
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Yes I agree. Maybe someone from production bioinfo is suitable to test the read aggregation epp?

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Test for ONT
https://ngi-lims-stage.scilifelab.se/clarity/work-details/1062119

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Test for AVITI
https://ngi-lims-stage.scilifelab.se/clarity/work-details/1062120

@kedhammar
Add new demux and seq steps, clean up variable names and comments
d7d5d1d
@kedhammar
remove try-except-KeyError block, it will never be used because of .g…
9ae0c05 
…et()
@kedhammar
Use f-string, remove superfluous .put() by using local var, improve docs
2249d63
@kedhammar
f-string
690baef
@kedhammar
clarify log+
1b806f6
@kedhammar
prettier big ints
c91ea53
@kedhammar
non-existing udf will actually not raise KeyError as described here
8dc758f
@kedhammar
renaming
53c4fd4
@kedhammar
refactor
8a20e20
@kedhammar
add comments and use local vars instead of udf access
5fa2523
@kedhammar
remove unused function
fd460d9
@kedhammar
refactor to reduce depth of nested loops, correct 10e6 to 1e6 for a m…
b714584 
…illion
@kedhammar
try using my wrapper, requires changing epp call
2011922
@kedhammar
change log file slot to summary, more accurate
1c01e20
@kedhammar
remove positional arg lims from main, defined globally
8b64c1f
@kedhammar
log formatting
0886bac
@kedhammar
process artifacts by name
3af2b75
@kedhammar
bugfix
f8fe788
@kedhammar
workout solution for ONT
94ea4d8
@kedhammar
add Illumina case
c3dcbda
@kedhammar
add unit
a43eb50
@kedhammar
add step config for AVITI and open-demux-steps failsafe
020be7a
@kedhammar
bump docs
a9659a7
@kedhammar kedhammar requested a review from alneberg January 17, 2025 14:00
alneberg
alneberg reviewed Jan 20, 2025
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scripts/readscount.py Outdated Show resolved Hide resolved
alneberg
alneberg approved these changes Jan 20, 2025
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@alneberg alneberg left a comment

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I think it looks good, but yes, this will need a verification as well.

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Verification 25_02_Rebuild and expand LIMS EPP for reads aggregation

@kedhammar
tweak docs
bef3088
@kedhammar
Merge commit '5ffa276f31a1c257ec82dad83ffe25fa5d92e231' into aggregat…
42ad826 
…e-reads
@kedhammar
replace hard exceptions with warnings
d0addab
@kedhammar
Global dicts are only used as value lists, so convert them to lists t…
9bde49e 
…o avoid discrepancy between keys (step IDs) on LIMS prod vs stage. Also remove unused list.
@kedhammar
- Ongoing steps will be counted, but warned against, so remove the so…
64415fb 
…rting function which will otherwise crash for ongoing steps.

- Add information whether the counts of a step are ongoing.

- Log the total read count for each tallied demux art
@kedhammar kedhammar requested a review from alneberg January 23, 2025 10:51
alneberg
alneberg approved these changes Jan 23, 2025
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Looks good! Very nicely done verification as well!

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@alneberg alneberg alneberg approved these changes

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@kedhammar @alneberg