Patch release 2.5.1 #541

jfy133 · 2023-11-13T08:17:23Z

First patch release for 2.5.0

### `Added`

### `Changed`

### `Fixed`

- [#489](https://github.com/nf-core/mag/pull/489) Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (reported by @tillenglert and @maxibor, fix by @maxibor)
- [#533](https://github.com/nf-core/mag/pull/533) Fix glob pattern for publishing MetaBAT2 bins in results (reported by @patriciatran, fix by @jfy133)
- [#535](https://github.com/nf-core/mag/pull/535) Fix input validation pattern to again allow direct FASTQ input (reported by @lennijusten, @emnilsson, fix by @jfy133, @d4straub, @mahesh-panchal, @nvnieuwk)

PR checklist

Fix input schema to allow direct input again

Remove 'dead' extension check code

github-actions · 2023-11-13T08:20:03Z

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

Posted for pipeline commit 4c3349d

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.5.1
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
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 WorkflowMag.groovy: Optionally add in-text citation tools to this list.
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ 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-mag_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-mag_logo_light.png
files_exist - File found: docs/images/nf-core-mag_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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowMag.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-mag_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 - .gitattributes matches the template
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-mag_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mag_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mag_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 - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.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 Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (227 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 2023-11-17 04:36:12

CHANGELOG.md

jfy133 · 2023-11-13T08:36:35Z

@nf-core-bot fix linting

d4straub

Looks good, but I dont understand some changes, added some remarks.

docs/output.md

modules/local/cat.nf

nextflow.config

subworkflows/local/gtdbtk.nf

workflows/mag.nf

pinin4fjords

I'm going to ditto all the comments made by @d4straub - I'd have made the same comments/ questions. But I'll trust you to resolve those before merge, so leaving my approval here.

nextflow_schema.json

maxulysse

No comments to add

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

jfy133 · 2023-11-15T13:52:56Z

OK - last issue is now with nf-validation. @nvnieuwk is on the case when he's back from holiday :D

CHANGELOG.md

maxibor and others added 30 commits August 25, 2023 16:48

fix: tracking of pre-processing in meta to handle downstream handling

fe5ff58

update gtdb-tk version

0ae55d2

update CAT

ecb7e99

cleanup: remove dump debugging

9069426

feat: check named results also includes refinement info

724c28d

cleanup: remove dumps

4947462

Merge branch 'custom' into custom2

0958404

feat: update gtdb-tk to 2.3.2

9a3de4f

doc: update output filenames

0886ca0

update GTDB-Tk module to 2.3.2

5a359f6

Merge branch 'custom2' of github.com:maxibor/mag into custom

8af91a7

Merge branch 'custom' of github.com:maxibor/mag into custom

498e5be

update GTDB-TK prefix

199ca1c

tmp: add dump for depth

e9428d0

update CAT

1da34ba

dump depth

01b2a03

remove duplicate bins

78b090f

fix: add depth

a501fe3

unique busco bins

3153e40

log: add busco dump

5da6c7d

fix: add missing config entries for concoct

611a53e

eukaryote bins are not sent to refined channel

e4ea756

debug: add dump for bin metrics

f9b4a36

debug: ch_filtered_bins -> bins

0a16911

debug: add groupTuple

7c94795

debug: flatten bins

73a14b5

debug: add bin_unbins dump

07c6dbd

debug: new combine for depths to avoid duplicated entries

548a03a

debug: add depths dump

12a2420

Bump versions post release

46cb244

jfy133 added 5 commits November 7, 2023 19:18

Merge pull request #537 from nf-core/fix-input-schema

f1cc2f3

Fix input schema to allow direct input again

Replace custom extension version with nextflow native

d68aaf7

Update changelog

a4475fb

Merge pull request #539 from nf-core/remove-dead-code

847a2da

Remove 'dead' extension check code

Bump versions for release

5c83236

jfy133 requested review from prototaxites, d4straub and CarsonJM November 13, 2023 08:18

Add missing dependency change

4077fdb

jfy133 commented Nov 13, 2023

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

a5c4095

[automated] Fix linting with Prettier

f16760c

d4straub reviewed Nov 13, 2023

View reviewed changes

pinin4fjords approved these changes Nov 13, 2023

View reviewed changes

maxulysse reviewed Nov 13, 2023

View reviewed changes

nextflow_schema.json Show resolved Hide resolved

maxulysse reviewed Nov 13, 2023

View reviewed changes

jfy133 and others added 3 commits November 13, 2023 11:18

Apply suggestions from code review

5f04c50

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Remove plugin pinning as not nf-core standardi

749c720

Harshil align pipeline version

62bc9dd

jfy133 requested review from maxulysse and d4straub November 13, 2023 11:13

d4straub approved these changes Nov 13, 2023

View reviewed changes

Merge branch 'dev' of github.com:nf-core/mag into dev

24d8f30

nvnieuwk mentioned this pull request Nov 16, 2023

Bug fix for file path patterns nextflow-io/nf-validation#132

Merged

jfy133 commented Nov 17, 2023

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

4c3349d

jfy133 merged commit e728900 into master Nov 17, 2023
31 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Patch release 2.5.1 #541

Patch release 2.5.1 #541

jfy133 commented Nov 13, 2023

github-actions bot commented Nov 13, 2023 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jfy133 commented Nov 13, 2023

d4straub left a comment

pinin4fjords left a comment

maxulysse left a comment

jfy133 commented Nov 15, 2023

Patch release 2.5.1 #541

Patch release 2.5.1 #541

Conversation

jfy133 commented Nov 13, 2023

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

jfy133 commented Nov 13, 2023

d4straub left a comment

Choose a reason for hiding this comment

pinin4fjords left a comment

Choose a reason for hiding this comment

maxulysse left a comment

Choose a reason for hiding this comment

jfy133 commented Nov 15, 2023

github-actions bot commented Nov 13, 2023 •

edited

Loading

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