Release 1.1.1 #354
Open
Release 1.1.1 #354
+364
−130
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
Bump version
Fix bbnorm memory
Bump version to 1.1.1 for release
|
vagkaratzas
approved these changes
Mar 12, 2025
| @@ -25,13 +24,20 @@ process BBMAP_BBNORM { | |||
| input = meta.single_end ? "in=${fastq.join(',')}" : "in=${fastq[0]} in2=${fastq[1]}" | |||
| output = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.nm.fastq.gz out2=${prefix}_2.nm.fastq.gz" | |||
|
|
|||
| memory = '-Xmx3g' | |||
There was a problem hiding this comment.
Maybe patch the updated nf-core modules to see differences than the original ones in their .diff files?
There was a problem hiding this comment.
This is the nf-core module, so I don't understand your comment.
There was a problem hiding this comment.
Oooh my bad! Thought you made this change for the pipeline. Go ahead :D
| @@ -4,8 +4,8 @@ process BBMAP_ALIGN { | |||
|
|
|||
| conda "${moduleDir}/environment.yml" | |||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |||
| 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' : | |||
| 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" | |||
| 'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' : | |||
There was a problem hiding this comment.
Shouldn't we prefer https over oras?
There was a problem hiding this comment.
Indeed. I just updated modules and got this, I'll fix the module.
lpantano
approved these changes
Mar 12, 2025
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.
PR checklist
nf-core pipelines 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).This release fixes a memory kill problem in BBNorm. I also updated some other modules.