Release 2.7.1 #660

d4straub · 2023-11-13T07:31:24Z

Release 2.7.1

This is a bug fix release to fix downstream analysis with QIIME2 that failed on some systems.

Changes are:

#655 - Added NUMBA_CACHE_DIR to fix downstream analysis with QIIME2 that failed on some systems
#656 - Moved conda-check to script-section and replaced exit 1 with error()
#657 - Corrected inaccurate reporting of QIIME2 taxonomic classifications and ASV length filtering
#657 - Improved parameter descriptions and sequence

PR checklist

Bump version to 2.8.0dev

…y instead of /tmp/

Fix nextflow version 23.10.0 with QIIME2

Move conda check to script section

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

Improve reporting

Prepare release 2.7.1

github-actions · 2023-11-13T07:33:49Z

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

Posted for pipeline commit bb23cb0

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.7.1
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
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 (260 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: branch.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.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' 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 2.10
Run at 2023-11-13 08:04:28

tillenglert

Minor suggestion/comment otherwise LGTM!

subworkflows/local/dada2_taxonomy_wf.nf

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

jannikseidelQBiC

Looks good to me as well!

d4straub · 2023-11-13T09:24:11Z

Thanks!

d4straub and others added 22 commits October 19, 2023 16:41

bump version to 2.8.0dev

16a8265

Merge pull request #651 from d4straub/prepare-2.8.0dev

ea50aeb

Bump version to 2.8.0dev

export MPLCONFIGDIR

4d334b9

change to tmp and export NUMBA_CACHE_DIR

8496c55

place XDG_CONFIG_HOME, MPLCONFIGDIR, NUMBA_CACHE_DIR in work director…

ac61247

…y instead of /tmp/

update CHANGELOG

b6b7928

replace tab with 4 spaces

ac8b05c

move conda check to script section

2326b7e

Merge pull request #655 from d4straub/fix-NXF_VER=23.10.0

f956dc1

Fix nextflow version 23.10.0 with QIIME2

Merge branch 'dev' into move-conda-checks

da06524

Merge pull request #656 from d4straub/move-conda-checks

35e980f

Move conda check to script section

fix QIIME2 taxonomy reporting

ba9b433

fix length filter reporting

0db5905

params docs: clarify --input_folder

e803b52

params docs: re-ordering and symbols

29ddd75

report: small optimisations in wording

83870b3

update CHANGELOG

b8ab349

Fix typo

76e3db7

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

Merge pull request #657 from d4straub/fix-reporting

e6e000d

Improve reporting

bump version to 2.7.1

2c5c0e9

update version in usage docs

b15b316

Merge pull request #659 from d4straub/prepare-release-2.7.1

a5e0dc3

Prepare release 2.7.1

d4straub requested review from tillenglert and jannikseidelQBiC November 13, 2023 07:32

tillenglert approved these changes Nov 13, 2023

View reviewed changes

subworkflows/local/dada2_taxonomy_wf.nf Outdated Show resolved Hide resolved

Update subworkflows/local/dada2_taxonomy_wf.nf

bb23cb0

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

jannikseidelQBiC approved these changes Nov 13, 2023

View reviewed changes

d4straub merged commit 113e90b into master Nov 13, 2023
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Release 2.7.1 #660

Release 2.7.1 #660

d4straub commented Nov 13, 2023 •

edited

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github-actions bot commented Nov 13, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

tillenglert left a comment

jannikseidelQBiC left a comment

d4straub commented Nov 13, 2023

Release 2.7.1 #660

Release 2.7.1 #660

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d4straub commented Nov 13, 2023 • edited Loading

PR checklist

github-actions bot commented Nov 13, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

tillenglert left a comment

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jannikseidelQBiC left a comment

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d4straub commented Nov 13, 2023

d4straub commented Nov 13, 2023 •

edited

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github-actions bot commented Nov 13, 2023 •

edited

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