Release 1.0 #219

danilodileo · 2023-12-07T13:01:44Z

PR checklist

PR for metatdenovo v1.0 release

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

Last PR before the release

github-actions · 2023-12-07T13:03:26Z

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

Posted for pipeline commit 3418d1f

+| ✅ 181 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ 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: 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-metatdenovo_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-metatdenovo_logo_light.png
files_exist - File found: docs/images/nf-core-metatdenovo_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/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/WorkflowMetatdenovo.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-metatdenovo_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: lib/nfcore_external_java_deps.jar
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
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.bbnorm_target= 100
nextflow_config - Config default value correct: params.bbnorm_min= 5
nextflow_config - Config default value correct: params.assembler= megahit
nextflow_config - Config default value correct: params.min_contig_length= 0
nextflow_config - Config default value correct: params.orf_caller= prodigal
nextflow_config - Config default value correct: params.prokka_batchsize= 10 MB
nextflow_config - Config default value correct: params.skip_eggnog= false
nextflow_config - Config default value correct: params.eggnog_dbpath= eggnog
nextflow_config - Config default value correct: params.skip_kofamscan= false
nextflow_config - Config default value correct: params.kofam_dir= ./kofam/
nextflow_config - Config default value correct: params.hmmpattern= *.hmm
nextflow_config - Config default value correct: params.skip_eukulele= false
nextflow_config - Config default value correct: params.eukulele_method= mets
nextflow_config - Config default value correct: params.eukulele_dbpath= ./eukulele/
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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
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-metatdenovo_logo_light.png matches the template
files_unchanged - docs/images/nf-core-metatdenovo_logo_light.png matches the template
files_unchanged - docs/images/nf-core-metatdenovo_logo_dark.png matches the template
files_unchanged - docs/README.md 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_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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (233 files)
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
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 2.12.1
Run at 2024-02-15 09:51:00

d4straub

Got 221/243 files, missing are subworkflows & workflow, might be able to do that tomorrow.
Looks good so far! I think my comments are all not critical. I might have commented what turned out later wasnt relevant, sorry for that.

README.md

assets/samplesheet.csv

modules/local/sum_kofamscan.nf

modules/local/sum_taxonomy.nf

nextflow.config

nextflow_schema.json

erikrikarddaniel · 2023-12-08T07:32:29Z

Thanks a bunch for that @d4straub ! Perfect to have something to work on.

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

Update README.md

Update nextflow.config

Update nextflow_schema.json

d4straub

Looks almost good to me.

In hindsight, to me as a reviewer, the biggest problem seems that the test that are existing are not executed using ci.yml.

subworkflows/local/eggnog.nf

subworkflows/local/fastqc_trimgalore.nf

workflows/metatdenovo.nf

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

Fix eggnog download

subworkflows/local/eggnog.nf

workflows/metatdenovo.nf

collect log prokka in a proper way

…bworkflow removed param eggnog_dbpath from subworkflow

Test solving lint issue

README.md

conf/modules.config

mahesh-panchal · 2024-02-14T14:11:23Z

docs/usage.md


-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
+By default, the pipeline uses prodigal (`--orf_caller prodigal` ) to call genes/ORFs from the assembly.
+This is suitable for prokaryotes, as is the Prokka alternative (`--orf_caller prokka`).


Hasn't Prokka been succeeded by Bakta now?

I didn't hear about it and I was just looking at their documentation. I know prokka can handle metatranscriptome and it looks like bakta is made primarily for MAGs.

docs/usage.md

workflows/metatdenovo.nf

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

mahesh-panchal · 2024-02-15T09:35:43Z

By the way, you can use the files changed tab to add all suggestions to a single commit.

version missing

danilodileo · 2024-02-15T12:11:32Z

By the way, you can use the files changed tab to add all suggestions to a single commit.

ah ok, good to know 😅

Danilo Di Leo and others added 7 commits December 5, 2023 18:04

bump version

57fe23c

update modules

4b03fd7

nextflow schema

e2e36c1

nf-core lint

60f5258

eukulele biocontainer update

0f74d71

Update nextflow.config

9160116

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

Merge pull request #218 from danilodileo/release

5b77bcd

Last PR before the release

d4straub reviewed Dec 7, 2023

View reviewed changes

danilodileo and others added 12 commits December 8, 2023 12:54

Update README.md

471c6ef

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

Update README.md

dedf144

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

Update modules/local/sum_kofamscan.nf

448656c

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

Update README.md

174451f

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

Update modules/local/sum_taxonomy.nf

7cf45c9

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

Update modules/local/sum_taxonomy.nf

747f29b

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

Update README.md

f6e0401

Merge pull request #220 from nf-core/danilodileo-patch-1

49a2bf9

Update README.md

Update nextflow.config

05e194a

Merge pull request #221 from nf-core/danilodileo-patch-2

5da4ea5

Update nextflow.config

Update nextflow_schema.json

26c943e

Merge pull request #222 from nf-core/danilodileo-patch-3

31e37dc

Update nextflow_schema.json

d4straub reviewed Dec 8, 2023

View reviewed changes

danilodileo and others added 7 commits December 11, 2023 12:12

Update subworkflows/local/fastqc_trimgalore.nf

309fab2

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

Update subworkflows/local/fastqc_trimgalore.nf

ef211a0

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

Update subworkflows/local/fastqc_trimgalore.nf

415b457

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

Update subworkflows/local/eggnog.nf

45d1a09

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

changed assets/samplesheets.csv file

922e48b

Merge branch 'nf-core:dev' into dev

dc8c440

updated modules

f0202ba

erikrikarddaniel and others added 2 commits February 9, 2024 11:00

Remove commented line

99f75ce

Merge pull request #258 from erikrikarddaniel/fix-eggnog-download

54cb246

Fix eggnog download

danilodileo commented Feb 9, 2024

View reviewed changes

subworkflows/local/eggnog.nf Show resolved Hide resolved

mahesh-panchal reviewed Feb 12, 2024

View reviewed changes

workflows/metatdenovo.nf Outdated Show resolved Hide resolved

Danilo Di Leo and others added 11 commits February 12, 2024 14:22

collect log prokka in a proper way

4b66191

Merge pull request #259 from danilodileo/fix-prokka-log-bug

b045877

collect log prokka in a proper way

removed param eggnog_dbpath from subworkflow

494648b

explicit values for EGGNOG_DOWNLOAD output

9f1c06c

Merge pull request #260 from danilodileo/remove-dbpath-from-eggnog-su…

4a525b2

…bworkflow removed param eggnog_dbpath from subworkflow

Template update for nf-core/tools version 2.12.1

94bc66c

resolved conflicts

53e4c69

forgot conflict

cbc6a20

modules update

17f027f

added images from template

b0f6f93

Merge pull request #261 from danilodileo/test-solving-lint-issue

d5c5f9e

Test solving lint issue

danilodileo requested a review from mahesh-panchal February 14, 2024 09:30

mahesh-panchal approved these changes Feb 14, 2024

View reviewed changes

danilodileo and others added 8 commits February 15, 2024 10:13

Update README.md

0d09c15

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update README.md

38ca12f

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update conf/modules.config

7e5dc4c

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update docs/usage.md

5574262

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update docs/usage.md

ee41e16

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update docs/usage.md

92b7058

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update workflows/metatdenovo.nf

4263795

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Update docs/usage.md

4a0e7b3

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

Danilo Di Leo and others added 2 commits February 15, 2024 10:45

version missing

b5edbf2

Merge pull request #262 from danilodileo/few-more-updates-for-review

3418d1f

version missing

danilodileo merged commit 766abe9 into master Feb 15, 2024
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Release 1.0 #219

Release 1.0 #219

danilodileo commented Dec 7, 2023

github-actions bot commented Dec 7, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

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d4straub left a comment

erikrikarddaniel commented Dec 8, 2023

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mahesh-panchal Feb 14, 2024

danilodileo Feb 15, 2024

mahesh-panchal commented Feb 15, 2024

danilodileo commented Feb 15, 2024

Release 1.0 #219

Release 1.0 #219

Conversation

danilodileo commented Dec 7, 2023

PR checklist

github-actions bot commented Dec 7, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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erikrikarddaniel commented Dec 8, 2023

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mahesh-panchal Feb 14, 2024

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mahesh-panchal commented Feb 15, 2024

danilodileo commented Feb 15, 2024

github-actions bot commented Dec 7, 2023 •

edited

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

d4straub left a comment •

edited

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