Add nonpareil #417
Merged
Add nonpareil #417
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This comment was marked as outdated.
This comment was marked as outdated.
|
jfy133
commented
Nov 30, 2023
|
@nf-core-bot fix linting |
conf/test_falco.config
Outdated
There was a problem hiding this comment.
Should nonpareil be included here since the process NONPAREIL_NONPAREIL was included? If that's the case, also check other config files.
perform_shortread_redundancyestimation = false
There was a problem hiding this comment.
I meant that should we also include perform_shortread_redundancyestimation = false in this config file.
There was a problem hiding this comment.
I decided it wasn't necesary as switching to falco does not modify the input files going into NONPAREIL in any way, so saving 🐻❄️ by running one less step
jfy133
commented
Nov 30, 2023
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
LilyAnderssonLee
approved these changes
Nov 30, 2023
|
Is it the linting that touched so many files? It's a bit confusing, but Lili already approved so that's also fine 🙂 . |
This is nf-test for you... I added 3 modules and updated one. Each comes with the typical ~3 module files, but for each module an additional 3-4 for nf-test and the conda env file, so doubling each. And then I updated quite a few test configs 🤷♀️ |
|
Thanks @LilyAnderssonLee ! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Add nonpareil metagenome redundancy estimation
Includes non-standard MultiQC output: the tool using R to generate a extrapolation plot.
The output from this is either a PNG or a R S3/S4 object that stores the raw data. There is no way to export the 'extrapolated' data as it is calculated in the plotting function. Therefore it's not really possible to add to MultiQC as otherwise it would require reconstructing the R function in python, and would involve computation in the MultiQC step.
Instead I've gone with adding a custom MultiQC section that embeds the PNG in the plot.
Example report here:
multiqc.zip
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).