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Clean ESMFold outputs | --env flags for apptainer enginer#464

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JoseEspinosa merged 16 commits into
nf-core:devfrom
Australian-Structural-Biology-Computing:clean-esmfold-outputs
Feb 12, 2026
Merged

Clean ESMFold outputs | --env flags for apptainer enginer#464
JoseEspinosa merged 16 commits into
nf-core:devfrom
Australian-Structural-Biology-Computing:clean-esmfold-outputs

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@keiran-rowell-unsw
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@keiran-rowell-unsw keiran-rowell-unsw commented Feb 11, 2026 •
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Tidies ESMFold outputs, since the module doesn't generate un-wanted intermediates:

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions Bot commented Feb 11, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f938ab

+| ✅ 329 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  33 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_link
  • schema_description - No description provided in schema for parameter: rfam_full_region_link
  • schema_description - No description provided in schema for parameter: rfam_cm_link
  • schema_description - No description provided in schema for parameter: rnacentral_rfam_annotations_link
  • schema_description - No description provided in schema for parameter: rnacentral_id_mapping_link
  • schema_description - No description provided in schema for parameter: rnacentral_sequences_link
  • schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_bfd_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_path
  • schema_description - No description provided in schema for parameter: rosettafold2na_weights_path
  • local_component_structure - post_processing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold_all_atom_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_rosettafold2na_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_colabfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - aria2_uncompress.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_esmfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_helixfold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-12 08:37:19

@keiran-rowell-unsw keiran-rowell-unsw marked this pull request as ready for review February 11, 2026 05:15
@keiran-rowell-unsw keiran-rowell-unsw changed the title Clean ESMFold ouputputs and have container triton cache writeable Clean ESMFold outputs | pass container triton cache env to container Feb 11, 2026
JoseEspinosa
JoseEspinosa requested changes Feb 11, 2026
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I made a couple of comments. Also, there are merging conflicts, probably due to the changelog, that I am not allowed to fix on this repo.

Comment thread conf/modules_esmfold.config Outdated
Comment thread conf/modules_esmfold.config Outdated
@keiran-rowell-unsw
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keiran-rowell-unsw commented Feb 11, 2026 •
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I made a couple of comments. Also, there are merging conflicts, probably due to the changelog, that I am not allowed to fix on this repo.

Thanks! I've reverted so it's a a couple of simple publishDir changes.

I've wrapped the --env paths our container engine needs passed inside a check for apptainer or singularity.
Just confirmed it runs on UNSW's cluster, without having the change the container

@keiran-rowell-unsw keiran-rowell-unsw changed the title Clean ESMFold outputs | pass container triton cache env to container Clean ESMFold outputs Feb 11, 2026
@keiran-rowell-unsw keiran-rowell-unsw changed the title Clean ESMFold outputs Clean ESMFold outputs | --env flags for apptainer enginer Feb 12, 2026
JoseEspinosa
JoseEspinosa approved these changes Feb 12, 2026
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Thanks! LGTM 🚀

Comment thread conf/modules_esmfold.config
Comment on lines +17 to +20
workflow.containerEngine in ['singularity', 'apptainer'] ?
'--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' :
''
}
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Suggested change
workflow.containerEngine in ['singularity', 'apptainer'] ?
'--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' :
''
}
workflow.containerEngine in ['singularity', 'apptainer'] ?
'--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' :
''
}

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Not so important, will merge anyway and fix in any other pr

@JoseEspinosa JoseEspinosa merged commit d30acfa into nf-core:dev Feb 12, 2026
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@keiran-rowell-unsw keiran-rowell-unsw mentioned this pull request Feb 12, 2026
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@JoseEspinosa JoseEspinosa mentioned this pull request Mar 18, 2026
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