Doc fix (patch 0.10.1) by muffato · Pull Request #229 · sanger-tol/blobtoolkit

muffato · 2026-03-30T08:05:06Z

Closes #224

Updated the instructions for building the Uniprot database

PR checklist

Copilot

Pull request overview

Patch release to address #224 by updating the UniProt Reference Proteomes database build instructions (to avoid Diamond “Duplicate keys” errors), along with associated metadata/version bumps across the pipeline.

Changes:

Update docs/usage.md UniProt DB build steps to de-duplicate entries during FASTA + taxid map generation.
Bump pipeline version references from 0.10.0 → 0.10.1 across config/metadata/snapshots.
Add a 0.10.1 changelog entry and refresh citation metadata for the patch release.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
`docs/usage.md`	Adjusts UniProt Reference Proteomes build instructions to remove duplicates before `diamond makedb`.
`CHANGELOG.md`	Adds `0.10.1` release notes for the documentation fix.
`CITATION.cff`	Updates release metadata (version/title/date).
`nextflow.config`	Bumps manifest version to `0.10.1`.
`ro-crate-metadata.json`	Updates RO-Crate workflow URL/version to `0.10.1`.
`assets/multiqc_config.yml`	Updates the report link to the `0.10.1` GitHub release tag.
`.nf-core.yml`	Bumps template version to `0.10.1`.
`tests/default.nf.test.snap`	Updates expected workflow version string to `v0.10.1`.
`tests/nobusco.nf.test.snap`	Updates expected workflow version string to `v0.10.1`.
`tests/raw.nf.test.snap`	Updates expected workflow version string to `v0.10.1`.

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github-actions · 2026-03-30T08:22:45Z

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

Posted for pipeline commit ce93b82

+| ✅ 205 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  20 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
local_component_structure - nohit_list.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - generate_config.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - jsonify_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - compressblobdir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - create_bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - restructurebuscodir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - windowstats_input.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - run_blastn.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - collate_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - finalise_blobdir.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - view.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - minimap_alignment.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - blobtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - run_blastx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/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 - busco_diamond_blastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - coverage_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_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
files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
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/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: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
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/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
template_strings - template_strings
merge_markers - merge_markers

✅ 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: 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/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: tests/default.nf.test
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_ignored.config
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-blobtoolkit_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/WorkflowBlobtoolkit.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
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 0.10.1
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.image_format= png
nextflow_config - Config default value correct: params.blast_annotations= all
nextflow_config - Config default value correct: params.outdir= results
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nf_test_content - 'tests/nobusco.nf.test' contains outdir parameter
nf_test_content - 'tests/nobusco.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nobusco.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/raw.nf.test' contains outdir parameter
nf_test_content - 'tests/raw.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/raw.nf.test' snapshots a 'versions.yml' file
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/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 - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml 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
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.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: sanger_test.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - WINDOWSTATS_INPUT found in conf/base.config and Nextflow scripts.
base_config - BLOBTOOLKIT_WINDOWSTATS found in conf/base.config and Nextflow scripts.
base_config - FASTAWINDOWS found in conf/base.config and Nextflow scripts.
base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
base_config - BLAST_BLASTN found in conf/base.config and Nextflow scripts.
base_config - NOHIT_LIST found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - WINDOWMASKER_MKCOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - WINDOWMASKER_USTAT found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_HIC found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ILMN found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_CCS found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_CLR found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ONT found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - PIGZ_COMPRESS found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BUSCO_BUSCO found in conf/modules.config and Nextflow scripts.
modules_config - RESTRUCTUREBUSCODIR found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_BLASTP found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTOOLKIT_WINDOWSTATS found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTOOLKIT_CREATEBLOBDIR found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTOOLKIT_UPDATEBLOBDIR found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTOOLKIT_CHUNK found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTOOLKIT_UNCHUNK found in conf/modules.config and Nextflow scripts.
modules_config - NOHIT_LIST found in conf/modules.config and Nextflow scripts.
modules_config - BLAST_BLASTN found in conf/modules.config and Nextflow scripts.
modules_config - COMPRESSBLOBDIR found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTK_IMAGES found in conf/modules.config and Nextflow scripts.
modules_config - JSONIFY_TAXDUMP found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 0.10.1, nfcore_yml.version = 0.10.1

Run details

nf-core/tools version 3.5.2
Run at 2026-03-30 08:27:10

…eference proteomes

muffato self-assigned this Mar 30, 2026

Copilot AI review requested due to automatic review settings March 30, 2026 08:05

Copilot started reviewing on behalf of muffato March 30, 2026 08:05 View session

Copilot AI reviewed Mar 30, 2026

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Comment thread docs/usage.md Outdated

Comment thread CHANGELOG.md Outdated

Comment thread ro-crate-metadata.json

muffato added 2 commits March 30, 2026 09:24

Updated instructions to accommodate duplicated sequences in Uniprot R…

aec219e

…eference proteomes

Changelog update and version bump

ce93b82

muffato force-pushed the patch branch from c00ec78 to ce93b82 Compare March 30, 2026 08:25

prototaxites approved these changes Mar 30, 2026

View reviewed changes

muffato merged commit 8ad0f7a into main Mar 30, 2026
20 checks passed

muffato deleted the patch branch March 30, 2026 12:08

muffato added this to the v0.10.1 milestone Mar 30, 2026

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Doc fix (patch 0.10.1)#229

Doc fix (patch 0.10.1)#229
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nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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