feat: update hisat2 modules for strict syntax - #12838
Merged
Merged
Conversation
- Combine separate input tuples into single tuple for hisat2/build - Add val hisat2_memory_input to replace params.hisat2_build_memory - Update meta.yml to document new input signature - Update all tests to use new input format - Add test for splice-aware indexing with 3.GB memory threshold Generated by opencode
maxulysse
changed the title
Generated by opencode
- hisat2 2.2.2 → 2.2.3, samtools 1.23 → 1.24 (align)
- hisat2 2.2.2 → 2.2.3 (build)
- hisat2 2.2.1 → 2.2.2, samtools 1.20 → 1.24 (extractsplicesites)
- Update container URLs to community-cr-prod.seqera.io
- Apply strict syntax: ${var} interpolation, else on new line
Generated by opencode
Strandedness can be passed via ext.args instead. Also fixes missing def on ss variable. Generated by opencode
maxulysse
changed the title
maxulysse
changed the title
matthdsm
reviewed
Aug 31, 2026
matthdsm
reviewed
Aug 31, 2026
- Add .conda-lock files for amd64/arm64 - Add containers section to meta.yml for all 3 modules - Update extractsplicesites hisat2 2.2.2 → 2.2.3 - Update container URLs from fresh patch Generated by opencode
Member
Author
No problem with the disappearances of the meta.strandeness? |
Contributor
|
Not from me. can be set through |
mahesh-panchal
approved these changes
Aug 31, 2026
mahesh-panchal
left a comment
mahesh-panchal
left a comment
Member
There was a problem hiding this comment.
Aside from what could be infrastructure issues, looks good to me.
Member
There was a problem hiding this comment.
There's no corresponding arm build even though align has one
| scan_id: sc-734493ace7062424_1 | ||
| linux/arm64: | ||
| name: community.wave.seqera.io/library/hisat2:2.2.3--0b83b24baf5a98d0 | ||
| build_id: "" |
Member
There was a problem hiding this comment.
This looks like it has missing values
Member
Author
There was a problem hiding this comment.
I used the nf-core command for this, I'll report failures to tools
This was referenced Aug 31, 2026
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 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.
Summary
Update hisat2 modules to use strict Nextflow syntax, bump software versions, and refactor the build module's input signature.
Changes
hisat2/build input refactor
Combined three separate input tuples into a single tuple with an explicit memory parameter:
tuple val(meta), path(fasta),tuple val(meta2), path(gtf),tuple val(meta3), path(splicesites)tuple val(meta), path(fasta), path(gtf), path(splicesites)+val hisat2_memory_inputThe
hisat2_memory_inputreplaces the previousparams.hisat2_build_memoryreference, making the module self-contained.Version bumps
Container updates
All three modules now use
community-cr-prod.seqera.io(singularity) andcommunity.wave.seqera.io(docker) instead of the previous Galaxy/Seqera URLs.Strict syntax compliance
$variable→${variable}throughout all main.nf fileselse {moved to its own lineoptional:true→optional: truehisat2/align cleanup
Removed the built-in strandedness logic (
--rna-strandnessflags). Users can pass these viaext.argsinstead.Test updates
3.GBmemory thresholdsanitizeOutput()from nft-utils for cleaner, more readable snapshotsparams { outdir }blocks from testsTesting
Generated by opencode
Verified by @maxulysse