Add a feature to generate samplesheet for differentialabundance #546
Conversation
This file contains hidden or 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
jfy133
reviewed
Oct 15, 2024
conf/modules.config
Outdated
| pattern: '*.{tsv,csv,arrow,parquet,biom}' | ||
| ], | ||
| [ path: { "${params.outdir}/downstream_samplesheets/differentialabundance/"}, | ||
| mode: params.publish_dir_mode, |
There was a problem hiding this comment.
These should only be enabled if the --generate_samplesheet_xxxx parameters are used!
Comment on lines
+760
to
+761
| - `samplesheet.csv`: A samplesheet for each classifier. | ||
| - `matrix.csv`: The output from taxpasta. |
There was a problem hiding this comment.
I think you should copy here also the note beflow about hte missing conditions
|
|
||
| ch_colnames = Channel.of('sample') | ||
|
|
||
| channelToSamplesheet(ch_colnames, ch_list_for_samplesheet, "downstream_samplesheets/differentialabundance", "samplesheet_${samplesheet_name}" ) |
There was a problem hiding this comment.
Please see the latest function as in detaxizer! It's tweaked again (sorry about that!)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.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.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,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).