Release 0.8.0 #183

muffato · 2025-05-16T11:21:47Z

(Still waiting for #173)

Changes made this release

Runtime of the blast commands is now capped at 12 hours (add timeout statement #166)
Upgraded Busco and added an option to control the gene predictor used (Move CI to use miniprot #160, make miniprot as default #174, update busco version #181)
nf-core template upgrade (to version 3.2.1) (Important! Template update for nf-core/tools v3.2.0 #164, Important! Template update for nf-core/tools v3.2.1 #176)
Documentation fixes (broken links) (Fixed the broken link #175)
Ability to run without any read data (Support an empty samplesheet and more read checks #177)

PR checklist

Important! Template update for nf-core/tools v3.2.0

* Move CI to use miniprot * use metaeuk for non-test runs * Removed extra whitespace * Removed comment that applied to metaeuk * Removed extra whitespace --------- Co-authored-by: Matthieu Muffato <[email protected]>

Co-authored-by: Matthieu Muffato <[email protected]>

add timeout statement

Important! Template update for nf-core/tools v3.2.1

Co-authored-by: Matthieu Muffato <[email protected]>

update busco version

github-actions · 2025-05-16T11:23:10Z

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

Posted for pipeline commit e8c2043

+| ✅ 189 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  19 tests had warnings |!

❗ Test warnings:

local_component_structure - generate_config.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 - jsonify_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - nohit_list.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 - input_check.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 - busco_diamond_blastp.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 - finalise_blobdir.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 - coverage_stats.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 - blobtools.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 - run_blastn.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: .editorconfig
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/ci.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: 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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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: 0.8.0
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.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
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_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO 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: ci.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: template_version_comment.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: 3.2.1
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.2.1
Run at 2025-05-19 12:28:53

…branch)

Version bump, changelog, contribution metadata

This reverts commit 34c3518.

yumisims

looks good!

muffato and others added 30 commits March 28, 2025 13:11

Fixed the changelog

5327c13

Template update for nf-core/tools version 3.2.0

b635d60

Template update for nf-core/tools version 3.2.0

d6120ed

Merge branch 'dev' into nf-core-template-merge-3.2.0

bc3ddce

Merge pull request #164 from sanger-tol/nf-core-template-merge-3.2.0

12ee265

Important! Template update for nf-core/tools v3.2.0

Move CI to use miniprot (#160)

014b326

* Move CI to use miniprot * use metaeuk for non-test runs * Removed extra whitespace * Removed comment that applied to metaeuk * Removed extra whitespace --------- Co-authored-by: Matthieu Muffato <[email protected]>

add timeout statement

63d58d1

Testing ci

9a76d7a

roll back the changes

5079032

Update modules/nf-core/blast/blastn/main.nf

c95602e

Co-authored-by: Matthieu Muffato <[email protected]>

Update main.nf

fec23ba

Update main.nf

1dca0a5

Fixed the indentation

4807cbb

Temporary version downgrade to circumvent the CI failure

21a91e5

Update modules/nf-core/blast/blastn/main.nf

ba96828

Co-authored-by: Matthieu Muffato <[email protected]>

patch, config and error output

e5b1ef1

patch, config and error output

6b75256

Completely removed occurrences of the command_epilog

0112875

No need to consider the task attempt number any more

83ce5df

Merge pull request #166 from sanger-tol/timeout

d34da21

add timeout statement

make miniprot as default

d2600f8

add augustus option

c952283

lint

3fda98e

Template update for nf-core/tools version 3.2.1

0678604

Merge pull request #176 from sanger-tol/nf-core-template-merge-3.2.1

effad05

Important! Template update for nf-core/tools v3.2.1

Fixed the broken link

c0d2199

Fixed more broken links

5a1467c

Support an empty samplesheet

f5e4192

Default RO crate generated by nf-core 3.2

e24bcc7

Retrived contributor information from the nexflow manifest

32579bd

yumisims and others added 15 commits May 9, 2025 16:02

Update windowstats.nf

2cc0553

Update jsonify_taxdump.nf

0736317

Update conf/base.config

ed83cf9

Co-authored-by: Matthieu Muffato <[email protected]>

update busco

a219638

patch busco

76e0440

patch busco

23f53cd

test

04d1a52

reverted back to original

f88e4fa

Synchronised the busco module with nf-core and fixed the patch

58968b1

Should have been updated like the template

a1f5062

Merge pull request #181 from sanger-tol/busco_version_upgrade

1d73c53

update busco version

Added some documentation for the new Busco option

8ec3553

When will it happen ?

7b41549

Need to report the new versions

699881b

Updated the changelog

c62dca5

muffato self-assigned this May 16, 2025

muffato added 4 commits May 16, 2025 12:26

Reenabled the pipelines lint command (was wrongly tied to the master …

aca1eed

…branch)

Merge branch 'dev' into contribution_metadata

be735ad

Missing versions

1d2b106

Habemus pokemonum !

a4befe8

muffato mentioned this pull request May 19, 2025

Version bump, changelog, contribution metadata #173

Merged

10 tasks

Merge pull request #173 from sanger-tol/contribution_metadata

57efaac

Version bump, changelog, contribution metadata

muffato marked this pull request as ready for review May 19, 2025 12:09

muffato requested a review from yumisims May 19, 2025 12:09

muffato added 3 commits May 19, 2025 13:19

This line must not be commented out

34c3518

Revert "This line must not be commented out"

a246dbc

This reverts commit 34c3518.

This cannot be uncommented out because the remote file doesn't exist

e8c2043

yumisims approved these changes May 19, 2025

View reviewed changes

yumisims merged commit 03d1f11 into main May 19, 2025
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Release 0.8.0 #183

Release 0.8.0 #183

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muffato commented May 16, 2025 •

edited

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edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Release 0.8.0 #183

Release 0.8.0 #183

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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muffato commented May 16, 2025 •

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