Update MEGAHIT container URLs #3689
Closed
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
As per voutcn/megahit#360 pigz is not currently installed in the MEGAHIT biocontainer images (singularity: https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2 - docker: quay.io/biocontainers/megahit:1.2.9--h5b5514e_3). Therefore, the NF-Core module will fail to compress the contigs using pigz. This commit resolves the described fix.
adamrtalbot
reviewed
Aug 2, 2023
| --no-name \\ | ||
| -p $task.cpus \\ | ||
| $args2 \\ | ||
| gzip \\ |
There was a problem hiding this comment.
Was pigz included for a reason? I'd like to check before discarding.
There was a problem hiding this comment.
Pigz runs the compression taks faster (in parallel), but sadly it's not included in the docker image provided by the author. I have requested it to be added as well here: voutcn/megahit#360
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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Outdated suggestions cannot be applied.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.
Replace docker and singularity image URLs with current ones from biocontainers project.