Template update for nf-core/tools v3.0.1 #422

fellen31 · 2024-10-09T09:01:13Z

Closes #421

PR checklist

github-actions · 2024-10-09T11:45:16Z

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

Posted for pipeline commit ff30f83

+| ✅ 179 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/modules.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
modules_config - modules_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: 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/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: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.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.config
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-nallo_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/WorkflowNallo.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 0.4.0dev
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.skip_qc= false
nextflow_config - Config default value correct: params.skip_short_variant_calling= false
nextflow_config - Config default value correct: params.skip_assembly_wf= false
nextflow_config - Config default value correct: params.skip_mapping_wf= false
nextflow_config - Config default value correct: params.skip_methylation_wf= false
nextflow_config - Config default value correct: params.skip_repeat_calling= false
nextflow_config - Config default value correct: params.skip_repeat_annotation= false
nextflow_config - Config default value correct: params.skip_phasing_wf= false
nextflow_config - Config default value correct: params.skip_snv_annotation= false
nextflow_config - Config default value correct: params.skip_cnv_calling= false
nextflow_config - Config default value correct: params.skip_call_paralogs= false
nextflow_config - Config default value correct: params.skip_rank_variants= false
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/
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.preset= revio
nextflow_config - Config default value correct: params.variant_caller= deepvariant
nextflow_config - Config default value correct: params.sv_caller= severus
nextflow_config - Config default value correct: params.phaser= longphase
nextflow_config - Config default value correct: params.hifiasm_mode= hifi-only
nextflow_config - Config default value correct: params.parallel_alignments= 1
nextflow_config - Config default value correct: params.parallel_snv= 13
nextflow_config - Config default value correct: params.vep_cache_version= 110
nextflow_config - Config default value correct: params.deepvariant_model_type= PACBIO
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.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
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
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'
schema_params - Schema matched params returned from nextflow config
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: ci_master.yml
actions_schema_validation - Workflow validation passed: fix-linting.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
multiqc_config - assets/multiqc_config.yml found and not ignored.
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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - HIFIASM found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_MERGE found in conf/base.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: 3.0.1

Run details

nf-core/tools version 3.0.1
Run at 2024-10-10 07:17:01

…to template-merge

jemten

Quick update @fellen31 🚀
Tried to go though it but I might have missed some 😄

jemten · 2024-10-09T15:48:59Z

.gitpod.yml


 vscode:
  extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code


Commented out?

Yep, commented out in the new version of the template.

jemten · 2024-10-09T15:55:46Z

conf/modules.config

Is this file used?

No, good catch!

jemten · 2024-10-09T15:57:46Z

nextflow.config

+\033[0;34m   __ _  ___ _ __   ___  _ __ ___ (_) ___      _ __ ___   ___  __| (_) ___(_)_ __   ___
+\033[0;34m  / _` |/ _ \\ '_ \\ / _ \\| '_ ` _ \\| |/ __|____| '_ ` _ \\ / _ \\/ _` | |/ __| | '_ \\ / _ \\_____
+\033[0;34m | (_| |  __/ | | | (_) | | | | | | | (_|_____| | | | | |  __/ (_| | | (__| | | | |  __/_____|
+\033[0;34m  \\__, |\\___|_| |_|\\___/|_| |_| |_|_|\\___|    |_| |_| |_|\\___|\\__,_|_|\\___|_|_| |_|\\___|
+\033[0;34m  |___/      _____  __| | ___ _ __    / / __   __ _| | | ___
+\033[0;34m / __\\ \\ /\\ / / _ \\/ _` |/ _ \\ '_ \\  / / '_ \\ / _` | | |/ _ \\
+\033[0;34m \\__ \\\\ V  V /  __/ (_| |  __/ | | |/ /| | | | (_| | | | (_) |
+\033[0;34m |___/ \\_/\\_/ \\___|\\__,_|\\___|_| |_/_/ |_| |_|\\__,_|_|_|\\___/


jemten · 2024-10-09T16:01:34Z

workflows/nallo.nf

@@ -497,7 +497,7 @@ workflow NALLO {
    softwareVersionsToYAML(ch_versions)
        .collectFile(
            storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name:  ''  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',


Why the first ''?

Guess '' holds nf_core_ in nf-core pipelines.

I'll change it to nallo_.

jemten

👍

fellen31 · 2024-10-10T07:25:28Z

👍

Might a mistake in there that I have missed as well, but I'll merge.

fellen31 and others added 11 commits March 22, 2024 16:26

Initial template commit

8305665

Template update for nf-core/tools version 2.14.1

184d031

Prettier

b64de2d

Template update for nf-core/tools version 2.14.1

51cccce

Template update for nf-core/tools version 2.14.1

69e1297

Template update for nf-core/tools version 2.14.1

e066f31

Template update for nf-core/tools version 3.0.0

106fbaa

Template update for nf-core/tools version 3.0.0

c6ffcdb

Template update for nf-core/tools version 3.0.0

ae82293

merge template

a13a8f3

wip

2734b52

fellen31 force-pushed the template-merge branch from 4e6e0bf to b021386 Compare October 9, 2024 11:42

fellen31 force-pushed the template-merge branch from b021386 to 1c79c65 Compare October 9, 2024 12:31

modules

ef4b45e

fellen31 force-pushed the template-merge branch from 1c79c65 to ef4b45e Compare October 9, 2024 12:37

fellen31 and others added 2 commits October 9, 2024 14:38

Template update for nf-core/tools version 3.0.1

63962e9

Merge remote-tracking branch 'origin/nf-core-template-merge-3.0.1' in…

81c0180

…to template-merge

fellen31 changed the title ~~Template update for nf-core/tools v3.0.0~~ Template update for nf-core/tools v3.0.1 Oct 9, 2024

fellen31 marked this pull request as ready for review October 9, 2024 13:00

fellen31 requested a review from a team as a code owner October 9, 2024 13:00

Update CHANGELOG and docs

16059c8

jemten reviewed Oct 9, 2024

View reviewed changes

Review suggestions

2119d05

jemten approved these changes Oct 10, 2024

View reviewed changes

Delete conf/igenomes_ignored.config

ff30f83

fellen31 merged commit 8c345f7 into dev Oct 10, 2024
15 checks passed

fellen31 deleted the template-merge branch October 10, 2024 07:25

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Template update for nf-core/tools v3.0.1 #422

Template update for nf-core/tools v3.0.1 #422

fellen31 commented Oct 9, 2024

github-actions bot commented Oct 9, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jemten left a comment

jemten Oct 9, 2024

fellen31 Oct 10, 2024

jemten Oct 9, 2024

fellen31 Oct 10, 2024

jemten Oct 9, 2024

jemten Oct 9, 2024

fellen31 Oct 10, 2024

fellen31 Oct 10, 2024

jemten left a comment

fellen31 commented Oct 10, 2024

Template update for nf-core/tools v3.0.1 #422

Template update for nf-core/tools v3.0.1 #422

Conversation

fellen31 commented Oct 9, 2024

PR checklist

github-actions bot commented Oct 9, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jemten left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

jemten left a comment

Choose a reason for hiding this comment

fellen31 commented Oct 10, 2024

github-actions bot commented Oct 9, 2024 •

edited

Loading

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