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Split hifiasm#969

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sofiademmou merged 26 commits intogenomic-medicine-sweden:devfrom
sofiademmou:split_hifiasm
Apr 23, 2026
Merged

Split hifiasm#969
sofiademmou merged 26 commits intogenomic-medicine-sweden:devfrom
sofiademmou:split_hifiasm

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@sofiademmou sofiademmou commented Mar 27, 2026 •
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Description

This PR splits hifiasm into two processes (bin and assembly) so they can have different resources allocated and reduce computational cost.

This PR closes #130

Added

Changed

  • Split HIFIASM process in the GENOME_ASSEMBLY subworkflow into HIFIASM_BINS and HIFIASM_ASSEMBLY

Fixed

Removed

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github-actions Bot commented Mar 27, 2026

PR checklist

  • Please describe the purpose of this change, the problem it solves, why this approach was chosen, its impact, and link any relevant issue if it already contains this information.
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool, follow the pipeline conventions in the contribution docs.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including new tools and authors/contributors).

@sofiademmou sofiademmou marked this pull request as ready for review April 10, 2026 09:55
@sofiademmou sofiademmou requested a review from a team as a code owner April 10, 2026 09:56
fellen31
fellen31 reviewed Apr 15, 2026
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Awesome, looks good! Just a few questions/comments.

Comment thread conf/modules/genome_assembly.config Outdated
Comment thread subworkflows/local/genome_assembly/main.nf Outdated
Comment thread subworkflows/local/genome_assembly/main.nf Outdated
Comment thread conf/modules/genome_assembly.config Outdated
fellen31
fellen31 reviewed Apr 21, 2026
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Looks good overall! I wonder if there could be some small issues since the output files are no longer stable.

Comment thread subworkflows/local/genome_assembly/tests/main.nf.test Outdated
Comment thread conf/modules/genome_assembly.config Outdated
Comment thread subworkflows/local/genome_assembly/main.nf Outdated
fellen31
fellen31 reviewed Apr 22, 2026
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Nice that you were able to fix the snapshots! Just some very minor things, then this is ready!

Comment thread conf/modules/genome_assembly.config Outdated
Comment thread subworkflows/local/genome_assembly/tests/nextflow.config Outdated
Comment thread subworkflows/local/genome_assembly/main.nf
Comment on lines +102 to +107
.multiMap { meta, reads, ul_reads, yak_paternal, yak_maternal, bin_files ->
reads: [meta, reads, ul_reads]
bins: [meta, bin_files]
yak: [ meta, yak_paternal, yak_maternal ]
}
.set { ch_hifiasm_assembly_in }
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Maybe a nextflow lint -harshil-alignment -format on this file... I hope we can run it automatically soon 🤞

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@sofiademmou sofiademmou Apr 23, 2026

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Done ! :) Should I use it on all the main.nf files for nallo in the meantime to make sure they have the right format ?

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Thanks. There is an issue where it removes inline comments, so it's not perfect yet.. we will have to do it manually for a bit longer on the files we modify.

fellen31
fellen31 approved these changes Apr 23, 2026
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Great, LGTM! 🥳

Comment thread conf/modules/genome_assembly.config
}

withName: '.*:GENOME_ASSEMBLY:HIFIASM' {
withName: '.*:GENOME_ASSEMBLY:HIFIASM_ASSEMBLY|.*:GENOME_ASSEMBLY:HIFIASM_BINS' {
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@fellen31 fellen31 Apr 23, 2026

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👍

@sofiademmou sofiademmou merged commit c24ff07 into genomic-medicine-sweden:dev Apr 23, 2026
358 of 365 checks passed
@github-project-automation github-project-automation Bot moved this to Done in Nallo Apr 23, 2026
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Split hifiasm process in two

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@sofiademmou @fellen31