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feat: add fast_4stage_multimer.json configs#11

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amandazhuyilan wants to merge 1 commit intodevfrom
add-gpu-docker-config-to-dev
Open

feat: add fast_4stage_multimer.json configs#11
amandazhuyilan wants to merge 1 commit intodevfrom
add-gpu-docker-config-to-dev

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@amandazhuyilan
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@amandazhuyilan amandazhuyilan commented Feb 25, 2026

This PR adds a new BindCraft advanced settings preset at fast_4stage_multimer.json to support quicker iteration during local workflow testing for running workflows using freebindcraft with docker profile.

Reason for this change

  • Provides a lower-cost configuration for test/dev runs.
  • Reduces turnaround time when validating pipeline behavior and infrastructure setup.
  • Keeps the default preset unchanged for standard/production-style runs.

Example Run

nextflow run . \
  -profile docker \
  --input assets/samplesheet.csv \
  --outdir local-test-output \
  --bindcraft_container docker.io/australianbiocommons/freebindcraft:1.0.3 \
  --settings_advanced assets/bindcraft/fast_4stage_multimer.json \
  --project local

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Feb 25, 2026

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 9182351

+| ✅ 156 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗  27 tests had warnings |!
-| ❌   5 tests failed       |-
Details

❌ Test failures:

  • nextflow_config - Config default value incorrect: params.quote_char is set as " in nextflow_schema.json but is `` in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.project = za08`` not found in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.use_dgxa100 = False`` not found in nextflow.config.
  • schema_params - Default value for param project invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param use_dgxa100 invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in gadi_test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in gadi_test.config: Give any required params for the test so that command line flags are not needed
  • 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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!
  • schema_params - Schema param project not found from nextflow config
  • schema_params - Schema param use_dgxa100 not found from nextflow config

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-bindflow_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-bindflow_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-bindflow_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: validation.help.beforeText
  • nextflow_config - Config variable ignored: validation.help.afterText
  • nextflow_config - Config variable ignored: validation.summary.beforeText
  • nextflow_config - Config variable ignored: validation.summary.afterText
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-bindflow_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-bindflow_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-bindflow_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/bindflow/bindflow/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2026-02-25 21:45:47

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@amandazhuyilan