rpsblast module and test #9577
Open
rpsblast module and test #9577
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
mberacochea
reviewed
Dec 16, 2025
vagkaratzas
requested changes
Dec 16, 2025
Contributor
vagkaratzas
left a comment
vagkaratzas
left a comment
There was a problem hiding this comment.
Nice, left some comments!
| documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs | ||
| doi: 10.1016/S0022-2836(05)80360-2 | ||
| licence: ["US-Government-Work"] | ||
| identifier: "" |
Contributor
There was a problem hiding this comment.
I guess you can add the blast identifier here, since rpsblast is shipped with the main blast container, correct?
Author
There was a problem hiding this comment.
I got the message from nf-core that the blast identifier couldn't be found during the module creation. I have checked the other nf-core modules for blast and any of them have identifier. Where else can I check?
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
vagkaratzas
requested changes
Dec 17, 2025
| script "../../../wget/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ [id:'smart'], "https://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/Smart_LE.tar.gz" ] |
Contributor
There was a problem hiding this comment.
Add a comment with expected file size to be downloaded maybe?
Contributor
|
Awesome! In approval state now, but waiting for the new download module to replace |
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Outdated suggestions cannot be applied.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.
nf-core/modules pull request
This is a brand new module for rpsblast, a BLAST application that searches a protein query against the conserved domain database (CDD).
PR checklist
Reported in issue #
labelnf-core modules test <MODULE> --profile docker