First release - v1.0.0 - German Rollmops #221

jasmezz · 2023-02-08T14:07:01Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Co-authored-by: louperelo <[email protected]>

…scan into params_abricate

This reverts commit 1071055.

Add relevant parametrs for ABRicate

update ampir model parameters

Add more gecco parametrs

Release version bump

github-actions · 2023-02-08T14:09:34Z

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

Posted for pipeline commit adaa105

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.0.0'
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.
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ 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-funcscan_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-funcscan_logo_light.png
files_exist - File found: docs/images/nf-core-funcscan_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/NfcoreSchema.groovy
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/WorkflowFuncscan.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: .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-funcscan_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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_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/NfcoreSchema.groovy 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: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (148 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: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 2.7.2
Run at 2023-02-15 10:25:51

mirpedrol

Looks good! :) I left some small comments

CHANGELOG.md

CITATIONS.md

docs/output.md

nextflow.config

bin/comBGC.py

jfy133

Sorry, having to split this review into two - the github interface is starting to run glacially slow... I'm hoping by submitting this it'll clean up teh cache so I can continue without it takeing 10 sec between each tick

CHANGELOG.md

CITATIONS.md

nextflow_schema.json

jfy133

Sorry, having to split this review into two - the github interface is starting to run glacially slow... I'm hoping by submitting this it'll clean up teh cache so I can continue without it takeing 10 sec between each tick

jfy133

Vast majority are typo fixes or missing version mixings

Good work everyone! Almost over the hill for the fun coding part!

conf/modules.config

nextflow_schema.json

workflows/funcscan.nf

Activate institutional profiles

Co-authored-by: louperelo <[email protected]>

Co-authored-by: James A. Fellows Yates <[email protected]>

Update dev branch for dev->master merge

Darcy220606 and others added 30 commits December 21, 2022 14:04

Update nextflow_schema.json

2e3f265

Co-authored-by: louperelo <[email protected]>

Update nextflow.config

4e56f1c

Co-authored-by: louperelo <[email protected]>

Update nextflow.config

bf8510b

Co-authored-by: louperelo <[email protected]>

Add relevant parametrs for BAKTA

2b840ae

Merge branch 'nf-core:dev' into params_abricate

ceaf67a

Merge branch 'nf-core:dev' into params_ampir

c10ddcd

Merge branch 'nf-core:dev' into params_amrfinderplus

671d7b2

Merge branch 'nf-core:dev' into params_antismash

6ce0442

Merge branch 'nf-core:dev' into params_bakta

8216d68

Merge branch 'nf-core:dev' into params_deepbgc

3911ad4

Merge branch 'nf-core:dev' into params_fargene

caced9c

Merge branch 'nf-core:dev' into params_gecco

e315a6c

Merge branch 'nf-core:dev' into params_prodigal

b40deaa

Merge branch 'nf-core:dev' into params_prokka

76383cb

Merge branch 'nf-core:dev' into params_rgi

1ca88da

Fix nf-core schema [skip ci]

d8c06fb

Fix nf-core schema

1207726

Merge branch 'params_abricate' of https://github.com/Darcy220606/func…

3a40538

…scan into params_abricate

Add uodate to schema

92a482d

Fix linting probs

7de9273

Update antismash lite and remove need for enable_conda

ef6871c

Add local mocule (draft)

1c921c1

Fetch modules update

5859bca

Try different system that does similar thing...

1071055

Revert "Try different system that does similar thing..."

5838f6c

This reverts commit 1071055.

Merge pull request #176 from Darcy220606/params_abricate

49075aa

Add relevant parametrs for ABRicate

Merge branch 'nf-core:dev' into params_ampir

f28af72

Merge pull request #164 from Darcy220606/params_ampir

7a81627

update ampir model parameters

update prettier schema

016ba30

Merge pull request #165 from Darcy220606/params_gecco

a34d73f

Add more gecco parametrs

jasmezz added 2 commits February 8, 2023 15:05

[skip ci] Merge pull request #220 from nf-core/release-version-bump

1bcacac

Release version bump

Merge branch 'master' into dev

d77f473

jfy133 assigned mirpedrol and jfy133 Feb 8, 2023

mirpedrol approved these changes Feb 9, 2023

View reviewed changes

jasmezz commented Feb 9, 2023

View reviewed changes

bin/comBGC.py Outdated Show resolved Hide resolved

jfy133 changed the title ~~First release~~ First release - v1.0.0 - German Rollmops Feb 13, 2023

jfy133 requested changes Feb 13, 2023

View reviewed changes

jfy133 self-requested a review February 13, 2023 12:23

jfy133 requested changes Feb 13, 2023

View reviewed changes

jasmezz and others added 15 commits February 13, 2023 15:55

Apply suggestions from dev->master code review

2f25998

Add indentation

6a886e1

Fix modules.config

20835d9

Remove curly brackets around args list elements

bb5e50e

Update nextflow.config

75dd5e3

Merge pull request #223 from nf-core/activate-institutional-profiles

fd09d8b

Activate institutional profiles

Apply suggestions from code review

99917c3

Fix variable evaluation in modules.config

5cdc300

[automated] Fix linting with Prettier

f86fd1e

Update conf/modules.config

96d39a5

Co-authored-by: louperelo <[email protected]>

Linting

56ea223

Fianly Fixes from review except DRAMP which publishDir isn't playing nic

84d986b

Apply suggestions from code review

776ffa8

Co-authored-by: James A. Fellows Yates <[email protected]>

Tiny typo fix

6a51152

Merge pull request #222 from nf-core/review-suggestions

adaa105

Update dev branch for dev->master merge

jfy133 self-requested a review February 15, 2023 10:29

jfy133 approved these changes Feb 15, 2023

View reviewed changes

jasmezz merged commit d6773ca into master Feb 15, 2023

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First release - v1.0.0 - German Rollmops #221

First release - v1.0.0 - German Rollmops #221

jasmezz commented Feb 8, 2023

github-actions bot commented Feb 8, 2023 •

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❗ Test warnings:

✅ Tests passed:

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First release - v1.0.0 - German Rollmops #221

First release - v1.0.0 - German Rollmops #221

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jasmezz commented Feb 8, 2023

PR checklist

github-actions bot commented Feb 8, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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github-actions bot commented Feb 8, 2023 •

edited

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