Add reference recommendations to usage docs #1314
Open
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
Dev -> master for 3.14.0 release
Sentence per line to allow easier commenting.
|
I've opened this a draft as I think it would be good to get more comments etc. before merging. Most of the checklist didn't seem relevant for a docs only change and I wasn't sure how to edit |
pinin4fjords
requested changes
Jun 11, 2024
There was a problem hiding this comment.
Good suggestions on content, but much of this is already covered, if at a lower level of detail, in the pre-existing material.
I've suggested some minor improvements to flow etc of your additions, but in general these need to be worked into existing sections to make sure we're not repeating ourselves.
This was just a bit of an information dump to start with but I agree it makes sense to combine with what is already there. I guess I overlooked it because it is an "options" section further down and I figured that was more about the technical details of the different arguments and not so much the broader question of which genome/annotation to use. Could we move the combined section closer to the start as it's likely to be relevant to more users than the options sections? |
Let's postpone reorganisation for a future PR (@drpatelh may have views), and stick with the new content integration for the moment. |
Co-authored-by: Jonathan Manning <[email protected]>
|
@pinin4fjords I've incorporated your suggestions and moved the new content to the existing sections |
There was a problem hiding this comment.
Just some more tweaks, then we probably need @drpatelh to approve.
Co-authored-by: Jonathan Manning <[email protected]>
|
Thanks alot for this @lazappi ! We will include it in the next release! Would love for @tdanhorn @MatthiasZepper to give this a once over too since they were involved in discussions in the parent issue. PS: I also sent you an invite to become a member of the nf-core community on Github. Hopefully, future contributions won't have to be approved on PRs. |
MatthiasZepper
approved these changes
Jul 3, 2024
There was a problem hiding this comment.
This is a really nice write-up and summary! I think the pipeline will profit greatly from this additional documentation. The only concern that I have is using the toplevel assemblies directly.
On the other hand, the quantification may be good enough and the impact not as big as I presume.
Co-authored-by: Matthias Zepper <[email protected]>
|
pinin4fjords
requested changes
Jul 10, 2024
| More information and links to further resources are [available from Ensembl](https://www.ensembl.org/info/website/upload/gff.html). | ||
| ::: | ||
|
|
||
| ### Reference transcriptome |
There was a problem hiding this comment.
Suggested change
| ### Reference transcriptome | |
| #### Reference transcriptome |
|
|
||
| We recommend not providing a transcriptome FASTA file and instead allowing the pipeline to create it from the provided genome and annotation. Similar to aligner indexes, you can save the created transcriptome FASTA and BED files to a central location for future pipeline runs. This helps avoid redundant computation and having multiple copies on your system. Ensure that all genome, annotation, transcriptome, and index versions match to maintain consistency. | ||
|
|
||
| ### Indices |
There was a problem hiding this comment.
Suggested change
| ### Indices | |
| #### Indices |
| #### Gencode | ||
| Remember to note the genome and annotation versions as well as the versions of the software used for indexing, as an index created with one version may not be compatible with other versions. | ||
|
|
||
| ### GENCODE |
There was a problem hiding this comment.
Suggested change
| ### GENCODE | |
| #### GENCODE |
| #### Prokaryotic genome annotations | ||
| As well as the standard annotations, GENCODE also provides "basic" annotations, which include only representative transcripts, but we do not recommend using these. | ||
|
|
||
| ### Prokaryotic genome annotations |
There was a problem hiding this comment.
Suggested change
| ### Prokaryotic genome annotations | |
| #### Prokaryotic genome annotations |
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.
Adds a section to the usage docs providing more information and recommendations about reference files. Fixes #1086.
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).