Template update #165

luisas · 2024-10-10T08:32:33Z

PR checklist

Template update PR

…lign into template-update

github-actions · 2024-10-15T08:21:58Z

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

Posted for pipeline commit f4a462e

+| ✅ 206 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

schema_params - Schema param genome not found from nextflow config
schema_params - Schema param fasta not found from nextflow config

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
multiqc_config - multiqc_config

✅ 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-multiplesequencealign_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-multiplesequencealign_logo_light.png
files_exist - File found: docs/images/nf-core-multiplesequencealign_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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-multiplesequencealign_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowMultiplesequencealign.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.version ends in dev: 1.1.0dev
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.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.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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-multiplesequencealign_logo_light.png matches the template
files_unchanged - docs/images/nf-core-multiplesequencealign_logo_light.png matches the template
files_unchanged - docs/images/nf-core-multiplesequencealign_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CALCULATE_SEQSTATS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SEQSTATS found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_PLDDT found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_PLDDT found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_SEQREFORMAT_SIM found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SIMSTATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - FAMSA_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - CLUSTALO_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - MAGUS_GUIDETREE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_TCOFFEETEMPLATE found in conf/modules.config and Nextflow scripts.
modules_config - CLUSTALO_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - MTMALIGN_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - CONSENSUS found in conf/modules.config and Nextflow scripts.
modules_config - PIGZ_COMPRESS found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALNCOMPARE_SP found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALNCOMPARE_TC found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - CALC_GAPS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_IRMSD found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_GAPS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_SP found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_TC found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_TCS found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_TCS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_EVAL found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS_EVAL found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - PREPARE_SHINY found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-10-24 13:40:30

mirpedrol

I made some style comments.
But mostly, I am not sure if the template update removed all your patch files from modules, so please make sure that everything is as it should be 🙂
After this is addressed, LGTM 🚀

.gitignore

CHANGELOG.md

modules.json

modules/nf-core/fastqc/environment.yml

modules.json

modules/nf-core/tcoffee/align/main.nf

nextflow.config

subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf

workflows/multiplesequencealign.nf

luisas · 2024-10-24T13:27:52Z

I made some style comments. But mostly, I am not sure if the template update removed all your patch files from modules, so please make sure that everything is as it should be 🙂 After this is addressed, LGTM 🚀

Thanks a lot for the review!!

Co-authored-by: Júlia Mir Pedrol <[email protected]>

…/main.nf Co-authored-by: Júlia Mir Pedrol <[email protected]>

…equencealign into template-update

nf-core-bot and others added 10 commits October 8, 2024 12:31

Template update for nf-core/tools version 3.0.0

e167ae7

Template update for nf-core/tools version 3.0.1

3d6f5bd

fixes_merge

941b76f

Merge branch 'dev' into template-update

95fd638

update config

77d3f07

Merge branch 'template-update' of github.com:luisas/multiplesequencea…

9d2d7e3

…lign into template-update

update

2647736

fix ignore

d3915de

Template update for nf-core/tools version 3.0.2

5037b41

fix template merge

99ecd54

luisas added 19 commits October 15, 2024 10:27

update modules

ea422d7

update modules

f38f13d

update modules

bd7971b

fix linting

6ac894f

fix linting

b0c2184

fix linting

c4735c0

fix linting

7209a81

fix linting

851746c

fix linting

2b22157

update schema

c742729

update

76d5144

update

3ef3a3a

update

b30c1e6

fix lint

79c5fc9

fix lint

63c2bbf

update

25387e0

retrigger

149accc

pulltimeout

57b0164

up

9d5513a

luisas added 7 commits October 21, 2024 08:09

u-

f2f693a

up

8902e2a

up

b7ed0dc

test

2da0d4b

update ci tests

dbc8d36

update

8853b36

fix

8f6aac1

mirpedrol approved these changes Oct 24, 2024

View reviewed changes

luisas and others added 6 commits October 24, 2024 15:28

Update CHANGELOG.md

1b43c71

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update modules.json

862d277

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update workflows/multiplesequencealign.nf

7318f0f

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Update subworkflows/local/utils_nfcore_multiplesequencealign_pipeline…

d24a90f

…/main.nf Co-authored-by: Júlia Mir Pedrol <[email protected]>

review

5372adc

Merge branch 'template-update' of https://github.com/luisas/multiples…

f4a462e

…equencealign into template-update

luisas merged commit 783b1d2 into nf-core:dev Oct 24, 2024
16 checks passed

luisas deleted the template-update branch January 27, 2025 11:07

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Template update #165

Template update #165

luisas commented Oct 10, 2024

github-actions bot commented Oct 15, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

luisas commented Oct 24, 2024

Template update #165

Template update #165

Conversation

luisas commented Oct 10, 2024

PR checklist

github-actions bot commented Oct 15, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mirpedrol left a comment

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luisas commented Oct 24, 2024

github-actions bot commented Oct 15, 2024 •

edited

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