Some fixes before the upcoming release #257
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…obs_name_col optional in report.rmd
WackerO
changed the title
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Is it necessary to "unbump" the versions? |
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…ybe it works online?
…nd messed them up
pinin4fjords
requested changes
Apr 2, 2024
nextflow_schema.json
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| @@ -268,8 +268,9 @@ | |||
| "properties": { | |||
| "proteus_measurecol_prefix": { | |||
| "type": "string", | |||
| "default": "LFQ intensity ", | |||
| "description": "Prefix of the column names of the MaxQuant proteingroups table in which the intensity values are saved; the prefix has to be followed by the sample names that are also found in the samplesheet. Default: 'LFQ intensity '; take care to also consider trailing whitespace between prefix and samplenames." | |||
| "default": "LFQ intensity_s", | |||
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This seems weird and brittle- too hacky for me. People are going to misunderstand this and get it wrong. We need a different solution - why not just make the proteus module allow for an optional space after the prefix?
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I generally prefer not having my code assume that a whitespace is necessary and instead just take directly what the user inputs...but I suppose here, the flexible whitespace addition is the best solution. I just updated the proteus module with those changes
Co-authored-by: Jonathan Manning <[email protected]>
Co-authored-by: Jonathan Manning <[email protected]>
Co-authored-by: Jonathan Manning <[email protected]>
…ntialabundance into prerelease_fixes
…o python); undid the changes to the docs/defaults for --proteus_measurecol_prefix regarding the final space
…into prerelease_fixes
pinin4fjords
requested changes
Apr 22, 2024
modules/local/filter_difftable.nf
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| @@ -2,10 +2,10 @@ process FILTER_DIFFTABLE { | |||
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| label 'process_single' | |||
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| conda "conda-forge::gawk=5.1.0" | |||
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Re-writing this process in Python is a quite a major change to smuggle into a PR of small fixes ;-).
Can you say why the process was re-written, and demonstrate that the output is the same relative to previous?
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If you prefer, I can also do the module change in a separate PR, that's not a problem!
Nope, can't demonstrate that, the output changed; it was incorrect before, that's why I had to change it :') AWK suddenly filtered out all the genes and just produced an empty table (was not the case when I originally added the module).
I tried a lot to change it in AWK but it simply did not work and I have to be honest, I found the AWK code quite painful to deal with as I'm simply not experienced enough with it.
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Oh, but as a follow-up, I did check the output. The new module + this code makes it so that the results are the same as the DE genes according to the html report, see here:
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Actually, could you raise this as a separate PR? I think that would make more sense and you can post the reasoning and the evidence there.
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Yes of course, see #264
10 tasks
…into prerelease_fixes
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added maxquant profile to nextflow.config, clarified some docu, made obs_name_col optional in report.rmd,
fixed FILTER_DIFFTABLE module (changed to python as AWK stopped filtering correctly)(done in #264)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).