Big Bakta update #235
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Big Bakta update #235
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louperelo
reviewed
Mar 6, 2023
nextflow.config
Outdated
| @@ -27,23 +27,25 @@ params { | |||
| annotation_prodigal_forcenonsd = false | |||
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| annotation_bakta_db = null | |||
| annotation_bakta_db_light = null | |||
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I am a bit confused about the new parameter:
--annotation_bakta_db expects a path to a local DB (might be full or light, depends on what the user downloaded himself)
while --annotation_bakta_db_light determines in the modules.config, if in BAKTA_BAKTADBDOWNLOAD the ext.args --type will be set to full or light:
params.annotation_bakta_db_light ? '--type light' : '--type full'
Shouldn't this then be a boolean parameter with default false instead of null? If no path to an existing baktaDB ist given via --annotation_bakta_db, then the full bakta_db is downloaded unless annotation_bakta_db_light was set to true.
Do we want the light or the full version to be default when downloading?
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Ahh yes, that's why reviews are important :D The new parameter should of course be boolean.
I remember my reason for having null was that there was an issue with nf-core schema build when putting false as default, but forgot to check/fix that.
Default: I would go for full DB, but can test if there are big differences to the light DB in the output. If not, let's use light of course.
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Maybe consider renaming --annotation_bakta_db to make clear that this is for a local installation. Something like --annotation_bakta_db_path or --annotation_bakta_db_local?
I agree with the full db as default. Then the parameter --annotation_bakta_db_light can just stay as it is.
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I agree, we should disambiguate, and default should be set to a boolean not null. Another suggestion:
--annotation_bakta_downloadlightdb
--annotation_bakta_localdbpath
Or something?
jfy133
requested changes
Mar 8, 2023
nextflow.config
Outdated
| @@ -27,23 +27,25 @@ params { | |||
| annotation_prodigal_forcenonsd = false | |||
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| annotation_bakta_db = null | |||
| annotation_bakta_db_light = null | |||
There was a problem hiding this comment.
I agree, we should disambiguate, and default should be set to a boolean not null. Another suggestion:
--annotation_bakta_downloadlightdb
--annotation_bakta_localdbpath
Or something?
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Mar 8, 2023
louperelo
approved these changes
Mar 9, 2023
jfy133
requested changes
Mar 10, 2023
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I agree with Lousia, I find the current parameters too similar in the naming scheme, which I Worry may confuse people that they are for related functions (e.g. maybe _local means download the full database, as it has the same camel case structure as indicating the download type).
Alternatively, we could replace the boolean for the light with a string:
--annotation_bakta_db_localpath '/path/to/'
--annotation_bakta_db_downloadtype 'light' ## where default is 'full'
Other than the naming, I think the code looks fine 👍
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@nf-core-bot fix linting |
jfy133
approved these changes
Mar 10, 2023
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This was referenced Mar 27, 2023
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params.annotation_bakta_db_lightto be able to switch between the light (1.3 GB) and full (33.1 GB) version of the Bakta DBCloses #234
Closes #214
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).