Release 2.8.0 #690

d4straub · 2024-01-12T11:58:33Z

A bunch of additions and bug fixes accumulated again, so a release is justified again I think.

Main changes:

Three additional reference databases: --qiime_ref_taxonomy greengenes2 (prokaryotic 16S), --dada_ref_taxonomy phytoref (eukaryotic plastid 16S rRNA), --dada_ref_taxonomy zehr-nifh (Nitrogenase iron protein NifH)
New parameters --qiime_ref_tax_custom, --skip_qiime_downstream, and --dada_addspecies_allowmultiple
Bug fixes for using phyloseq, VSEARCH, error messages
Updated documentation & reporting
Pipeline template update

For details, please have a look at the CHANGELOG.

PR checklist

Bump version 2.7.1 to 2.8.0dev

…me database.

…stored in either a directory or a tarball.

…d to emit result to stdout.

… --qiime_ref_tax_custom and --classifier.

Co-authored-by: Daniel Straub <[email protected]>

…f_tax_custom.

…en-source-background-assets/ampliseq into qiime2_custom_db Conflicts: subworkflows/local/qiime2_preptax.nf workflows/ampliseq.nf

Merging template updates 2.11

Important! Template update for nf-core/tools v2.11.1

Greengenes2 2022.10 Support

fix conda package in FILTER_SSU

Co-authored-by: Till E. <[email protected]>

Update docs, citations and usage with new taxonomic reference databases

bump version to 2.8.0

github-actions · 2024-01-12T12:00:42Z

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

Posted for pipeline commit 2c67a45

+| ✅ 157 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.8.0
readme - README did not have a Nextflow minimum version badge.
schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: .gitattributes
actions_ci - actions_ci

✅ 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: CODE_OF_CONDUCT.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/CONTRIBUTING.md
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/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: assets/nf-core-ampliseq_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/images/nf-core-ampliseq_logo_light.png
files_exist - File found: docs/images/nf-core-ampliseq_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowAmpliseq.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-ampliseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md 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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-ampliseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-ampliseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-ampliseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
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.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (278 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.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' 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'

Run details

nf-core/tools version 2.11.1
Run at 2024-01-15 13:03:16

erikrikarddaniel

A single comment out of curiosity, otherwise 👍

modules/local/gzip_decompress.nf

tillenglert

Nitpicking, but looks good! :)

bin/taxref_reformat_zehr-nifh.sh

nextflow_schema.json

Reviewer comments 2.8.0

d4straub · 2024-01-15T15:35:04Z

Thanks!

d4straub and others added 30 commits November 13, 2023 12:38

bump version to 2.8.0dev

3b50902

update changelog

77bb7ec

fix indentation

2992fb7

Merge pull request #661 from d4straub/bump-version-2.7.1-to-2.8.0dev

1067c7c

Bump version 2.7.1 to 2.8.0dev

Add params.qiime_ref_tax_custom in preparation of allowing custom qii…

d86c569

…me database.

Implementation of logic to handle a custom qiime2 reference database …

439097c

…stored in either a directory or a tarball.

Add greengenes2 2022.10 to qiime ref databases.

d924110

Add greengenes2022 to acceptable qiime_ref_taxonomy values.

1082841

gzip does not operate on symbolic links unless forced or, as now, tol…

4612cd1

…d to emit result to stdout.

Some params checking logic.

14c89b9

Loose . lying around.

d214ec0

Only perform collect if going to FORMAT_TAXONOMY_QIIME.

9346d7a

Set into new channel when branching on ch_qiime_ref_taxonomy.£

ef053b1

Try to unpack the database dir into component files using a module.

a48a09f

Remove map wrapping the combine.

a9971b6

Remove unpack in favour of map and filter.

aac51bd

Glob results in list in all circumstances, check length instead.

1b2825e

Update usage.md.

c230c22

Merge remote-tracking branch 'upstream/dev' into greengenes_2022

4e32672

Update CHANGELOG.md.

1dd0d8e

Add pull request link to changelog.

850a603

Merge remote-tracking branch 'upstream/dev' into qiime2_custom_db

a903fbe

Update CHANGELOG.md.

a4219a0

Update error message when passing both one of --qiime_ref_taxonomy or…

0ccf6e6

… --qiime_ref_tax_custom and --classifier.

Update CHANGELOG.md with pull request number.

590f415

Co-authored-by: Daniel Straub <[email protected]>

Add support for specifying two (possibly gzipped) files as --qiime_re…

f5d80f5

…f_tax_custom.

Only support providing two files separated by a comma.

7016682

Fix split returns a String[] and we actually need an ArrayList.

79cbfe8

Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…

03881b2

…en-source-background-assets/ampliseq into qiime2_custom_db Conflicts: subworkflows/local/qiime2_preptax.nf workflows/ampliseq.nf

Move ch_ref_database set into correct scope.

6d767bc

d4straub and others added 17 commits December 20, 2023 14:22

update docker runOptions

1e14c0e

adjust pplace.nf.test.snap

9742624

Merge pull request #683 from d4straub/merging-template-updates-2-11

4b616ed

Merging template updates 2.11

Template update for nf-core/tools version 2.11.1

127b88a

Merge pull request #684 from nf-core/nf-core-template-merge-2.11.1

eadcd30

Important! Template update for nf-core/tools v2.11.1

merge dev

975e6d4

Apply suggestions from code review

815e62b

activate multi-cpu use in QIIME2_EXTRACT

70b2e01

Merge pull request #666 from MatthewJM96/greengenes_2022

1798c4a

Greengenes2 2022.10 Support

fix conda package in FILTER_SSU

54e3d60

update docs

06dcda7

Merge pull request #687 from d4straub/fix-FILTER_SSU-conda

591ac20

fix conda package in FILTER_SSU

Apply suggestions from code review

9dbb353

Co-authored-by: Till E. <[email protected]>

Merge pull request #688 from d4straub/update-docs-tax-databases

c92e172

Update docs, citations and usage with new taxonomic reference databases

bump version to 2.8.0

08cb7f0

fix prettier

24ab709

Merge pull request #689 from d4straub/bump-version-2.8.0

7ebd565

bump version to 2.8.0

d4straub requested a review from tillenglert January 12, 2024 12:09

erikrikarddaniel approved these changes Jan 12, 2024

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tillenglert approved these changes Jan 15, 2024

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d4straub added 5 commits January 15, 2024 10:10

update parameter help

0be678e

update qiime_ref_tax_custom help text

678ce1a

change qiime_ref_tax_custom test files to nf-core

5ad866f

replace local gzip with nf-core module pigz/uncompress

4694510

fix typo

08353dd

d4straub mentioned this pull request Jan 15, 2024

Reviewer comments 2.8.0 #691

Merged

10 tasks

Merge pull request #691 from d4straub/reviewer-comments-2-8-0

2c67a45

Reviewer comments 2.8.0

d4straub merged commit f3c97e1 into master Jan 15, 2024
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Release 2.8.0 #690

Release 2.8.0 #690

d4straub commented Jan 12, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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d4straub commented Jan 15, 2024

Release 2.8.0 #690

Release 2.8.0 #690

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d4straub commented Jan 12, 2024 • edited Loading

PR checklist

github-actions bot commented Jan 12, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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d4straub commented Jan 15, 2024

d4straub commented Jan 12, 2024 •

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