Add MiniBWA aligner by edmundmiller · Pull Request #221 · nf-core/nascent

edmundmiller · 2026-07-07T02:21:12Z

Summary

add MiniBWA as an aligner option
build MiniBWA+htslib+samtools containers with Wave
pipe MiniBWA output through samtools and reuse shared BAM sort/stats path
add MiniBWA docs, schema, citations, config, and nf-test coverage

Containers

Docker/Wave: community.wave.seqera.io/library/minibwa_htslib_samtools:6d867025b2559348
Singularity/Wave SIF: oras://community.wave.seqera.io/library/minibwa_htslib_samtools:8111e1ae64c560b2

Validation

nf-test test workflows/tests/aligner/minibwa.nf.test --profile debug,test,docker,wave --verbose
wave --inspect -i oras://community.wave.seqera.io/library/minibwa_htslib_samtools:8111e1ae64c560b2 -o json
nextflow config -profile test,singularity,wave
git diff --check

Note: local Singularity/Apptainer is not installed on this Mac, so the SIF was validated via Wave inspect rather than local execution.

nf-core-bot · 2026-07-07T02:21:46Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2026-07-07T21:17:22Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 0cb4c73

+| ✅ 166 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗  23 tests had warnings |!

Details

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
readme - README did not have an nf-core template version badge.
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 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
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 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 nextflow.config: Specify any additional parameters here
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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/nascent/nascent/subworkflows/local/prepare_genome.nf: _ versions = ch_versions.ifEmpty(null)
_
local_component_structure - bed2saf.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - quality_control.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .github/actions/get-shards/action.yml
files_exist - File is ignored: .github/actions/nf-test/action.yml
files_exist - File is ignored: tests/default.nf.test
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/nf-core-nascent_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nascent_logo_light.png
schema_params - schema_params

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-nascent_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-nascent_logo_light.png
files_exist - File found: docs/images/nf-core-nascent_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-nascent_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowNascent.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/images/nf-core-nascent_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
modules_config - MINIBWA_MAP found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - DRAGMAP_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_ found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_PILEUP found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_BAMCOVERAGE_PLUS found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_BAMCOVERAGE_MINUS found in conf/modules.config and Nextflow scripts.
modules_config - DREG_PREP found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_ found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_FINDPEAKS found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_MAKETAGDIRECTORY found in conf/modules.config and Nextflow scripts.
modules_config - HOMER_MAKEUCSCFILE found in conf/modules.config and Nextflow scripts.
modules_config - PINTS_CALLER found in conf/modules.config and Nextflow scripts.
modules_config - GROHMM_PARAMETERTUNING found in conf/modules.config and Nextflow scripts.
modules_config - GROHMM_TRANSCRIPTCALLING found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT found in conf/modules.config and Nextflow scripts.
modules_config - SUBREAD_FEATURECOUNTS_GENE found in conf/modules.config and Nextflow scripts.
modules_config - BED2SAF found in conf/modules.config and Nextflow scripts.
modules_config - SUBREAD_FEATURECOUNTS_PREDICTED found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.0.2
Run at 2026-07-12 04:37:12

edmundmiller force-pushed the add-minibwa-aligner branch 7 times, most recently from 9fba32d to f928fce Compare July 7, 2026 21:13

edmundmiller force-pushed the add-minibwa-aligner branch from f928fce to dee80d9 Compare July 7, 2026 21:34

edmundmiller mentioned this pull request Jul 8, 2026

Merge nf-core template 4.0.2 #223

Merged

edmundmiller added 2 commits July 11, 2026 23:26

Add MiniBWA aligner

7d8313e

fix(ci): guard Nextflow config parsing

3035956

edmundmiller force-pushed the add-minibwa-aligner branch from dee80d9 to 48b0708 Compare July 12, 2026 04:32

fix(ci): resolve nf-core lint failures

0cb4c73

edmundmiller force-pushed the add-minibwa-aligner branch from 48b0708 to 0cb4c73 Compare July 12, 2026 04:36

edmundmiller marked this pull request as ready for review July 12, 2026 04:39

edmundmiller merged commit f993c38 into dev Jul 12, 2026
13 of 36 checks passed

edmundmiller deleted the add-minibwa-aligner branch July 12, 2026 05:23

This was referenced Jul 12, 2026

revert: remove unverified MiniBWA integration #224

Closed

fix(test): use small reference for MiniBWA #225

Merged

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Add MiniBWA aligner - #221

Add MiniBWA aligner#221
edmundmiller merged 3 commits into
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add-minibwa-aligner

edmundmiller commented Jul 7, 2026

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edmundmiller commented Jul 7, 2026

Summary

Containers

Validation

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️