8000 Drop db_params patterns for bracken and kmcp by LilyAnderssonLee · Pull Request #476 · nf-core/taxprofiler · GitHub
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Drop db_params patterns for bracken and kmcp #476

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Merged
merged 3 commits into from
Apr 24, 2024
Merged

Drop db_params patterns for bracken and kmcp #476

merged 3 commits into from
Apr 24, 2024

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LilyAnderssonLee
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Fix the issue #475

The original definitions of db_params of bracken and kmcp in `db_check.nf``

    if ( row.tool == 'bracken' && row.db_params && !row.db_params.contains(";") )  error("[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon if passing parameter. Error in: ${row}")
    if ( row.tool == 'kmcp' && row.db_params && row.db_params.matches(".*;\$"))  error ("[nf-core/taxprofiler] ERROR: Invalid database db_params entry. KMCP only requires a semi-colon if passing arguments to KMCP profile, in cases of which the arguments should go after the semi-colon. Error in: ${row}")

The database.csv used in this test:

tool,db_name,db_params,db_path
bracken,db1,;-r 150,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/bracken/testdb-bracken.tar.gz
kraken2,db2,--quick,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz
kmcp,db1,;\$--min-kmers 30;\$--min-query-cov 0.5,https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kmcp/test-db-kmcp.tar.gz

The Bracken output files in this test:
image

kmcp output files in this test:
image

PR checklist

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@LilyAnderssonLee LilyAnderssonLee requested a review from jfy133 April 24, 2024 06:44
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github-actions bot commented Apr 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d6c5f75

+| ✅ 193 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-24 13:06:02

@jfy133
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jfy133 commented Apr 24, 2024

I'm trying work out the best way to do this now:

Reading our docs:

image

And comparing with the code, it looks like to me actually we don't require the ; even if you're running bracken. We did in the past but we relaxed: you only need a semi-colon if you want to supply to both kraken/bracken or just kraken. If you want to send to just kraken, no semi-0colon needed.

So in this case the new pattern wouldn't work with that, as it's requiringa semi-colon

Hence... I think we just need to remove the pattenr entirely? What do you think?

@LilyAnderssonLee
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It sounds wise to me to remove the db_parmas patters for bracken and kmcp.

@LilyAnderssonLee LilyAnderssonLee changed the title Correct db_params patterns of bracken and kmcp Drop db_params patterns for bracken and kmcp Apr 24, 2024
@jfy133 jfy133 merged commit e8ce046 into nf-core:dev Apr 24, 2024
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@jfy133
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jfy133 commented Apr 24, 2024

Thank you @LilyAnderssonLee ! I think we can do a patch release already (if you don't have time I will do it tomorrow evening)

@jfy133
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jfy133 commented Apr 24, 2024

Unless @sofstam would have time

@LilyAnderssonLee
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@jfy133 I have some time tomorrow morning before 10:00. I hope I can manage a patch release before then.

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sofstam commented Apr 24, 2024 via email

75A8

@LilyAnderssonLee LilyAnderssonLee deleted the database_schema_bug branch June 25, 2024 13:49
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