Adressing review suggestions for Version 1.0.0 #9

Felix-Kummer · 2024-08-13T08:20:45Z

Adding changes requested in review #8 for the first release of the Rangeland pipeline in nf-core #7 .

…essing results, some minor adjustments in the docs.

github-actions · 2024-08-13T08:22:17Z

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

Posted for pipeline commit a651b55

+| ✅ 202 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ 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.
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

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.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-rangeland_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-rangeland_logo_light.png
files_exist - File found: docs/images/nf-core-rangeland_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: .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-rangeland_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/WorkflowRangeland.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 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.sensors_level2= LND04 LND05 LND07
nextflow_config - Config default value correct: params.start_date= 1984-01-01
nextflow_config - Config default value correct: params.end_date= 2006-12-31
nextflow_config - Config default value correct: params.resolution= 30
nextflow_config - Config default value correct: params.indexes= NDVI BLUE GREEN RED NIR SWIR1 SWIR2
nextflow_config - Config default value correct: params.mosaic_visualization= true
nextflow_config - Config default value correct: params.pyramid_visualization= true
nextflow_config - Config default value correct: params.group_size= 100
nextflow_config - Config default value correct: params.publish_dir_enabled= true
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/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-rangeland_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rangeland_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rangeland_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
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: 'image/tiff, application/x-tar'
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: 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
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 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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FORCE_GENERATE_ANALYSIS_MASK found in conf/modules.config and Nextflow scripts.
modules_config - FORCE_GENERATE_TILE_ALLOW_LIST found in conf/modules.config and Nextflow scripts.
modules_config - FORCE_PREPROCESS found in conf/modules.config and Nextflow scripts.
modules_config - HIGHER_LEVEL_CONFIG found in conf/modules.config and Nextflow scripts.
modules_config - FORCE_HIGHER_LEVEL found in conf/modules.config and Nextflow scripts.
modules_config - FORCE_PYRAMID found in conf/modules.config and Nextflow scripts.
modules_config - FORCE_MOSAIC found in conf/modules.config and Nextflow scripts.
modules_config - CHECK_RESULTS found in conf/modules.config and Nextflow scripts.
modules_config - CHECK_RESULTS_FULL found in conf/modules.config and Nextflow scripts.
modules_config - PREPROCESS_CONFIG found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_ 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 2024-11-26 14:58:33

…iles

.gitignore

.nf-core.yml

mashehu · 2024-11-26T14:20:33Z

docs/usage.md

+--mosaic_visualization  = '[boolean]'
+--pyramid_visualization = '[boolean]'


Suggested change

--mosaic_visualization = '[boolean]'

--pyramid_visualization = '[boolean]'

mosaic_visualization = 'true'

pyramid_visualization = 'true'

maybe also add a title=paramters.yml to the code block and switch the language. for reproducibility I would discourage cli paramter input and nudge people to use a paramter file instead.

I would need to change that for every parameter in usage.md
Previously I was told to use cli parameter input.
Is there a guideline for that?

mashehu · 2024-11-26T14:20:51Z

docs/usage.md

+--save_ard  = '[boolean]'
+--save_tsa  = '[boolean]'


same as above

mashehu · 2024-11-26T14:21:36Z

docs/usage.md

-The default value is 2.
+### Module output publishing
+
+Certain users may not be interested in the pipeline's outputs.


why would one want to run a pipeline, while not being interested in the outputs? 🤔

This was requested by a colleague for evaluating workflow execution approaches using different task placement strategies.

docs/usage.md

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Felix-Kummer added 3 commits August 7, 2024 15:11

Implemented minor reviewer requests

443ba0a

Added parameters to control publishing behavior for intermediate proc…

3dca391

…essing results, some minor adjustments in the docs.

Added descriptions to custom scripts.

a5df347

Felix-Kummer changed the title ~~Adressing review suggestions~~ Adressing review suggestions for Version 1.0.0 Aug 13, 2024

Felix-Kummer added 25 commits August 21, 2024 15:15

Applied more minor changes requested by the reviewers

2e208fc

Reworked merge scripts

e5d4425

Added authors and licenses to scripts

fd29a4b

Removed unused sensors_level1 parameter

e042a1c

Applied one-sentence-per-line-scheme in .md files

69fd493

Removed unnecessarily ignored parameters in test profile

17db3ba

Improved parameter references in docs

4a7518b

Replaced retry strategies with error_retry label

4949334

Adopted nf-core pseudo-standard directory structure for local modules

d7ba83b

Updated nf-core untar module

64c909a

Enriched schema with patterns for parameters

5e006c0

Improved output documentation for tss files

980347f

Added date format to date parameters

e036cb3

Removed deprecated docker parameter

7564dd6

Added tags to all modules

cd5fb92

Removed restrictions on FORCE thread numbers and corresponding parameter

f12f0c9

Replaced usage of params in modules and subworkflows with channels

7f7805b

Added more output channels to the top level workflow

fd09671

Added automatic tarball extraction for input parameters

a4d2e7f

Changed UNTAR container to its default container image

99ff909

Changed force-pyramid to process a single file instead of groups of f…

605f154

…iles

Merge branch 'nf-core:dev' into dev

ac70e35

Merge remote-tracking branch 'origin/dev' into dev

b6c2e63

Updated input mimetype in schema

22166e9

Added missing fields to schema

c822ba7

Felix-Kummer added 9 commits October 25, 2024 11:07

Updated changelog

15e4c1e

Fixed some linter warnings

415edb4

Replaced for-loops with GNU parallel

0585e5e

Migrated check result modules to nf-test

bd82d81

Added parameter to disable all output publishing

a8da0e3

Fixed log output for preprocessing

e67107d

Added pipeline-level nf-test tests

88ea70f

Aligned run command in usage docs with other pipelines

72996b1

Updated nf-core workflows and modules

ba1d17f

mashehu approved these changes Nov 26, 2024

View reviewed changes

Felix-Kummer and others added 3 commits November 26, 2024 15:32

Fix nf-test entry in .gitignore

d8be4ef

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Fixed wrong pipeline version in usage.md

3d64227

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Added concrete boolean values for parameters in usage.md

a651b55

Felix-Kummer merged commit caee766 into nf-core:dev Nov 26, 2024
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Adressing review suggestions for Version 1.0.0 #9

Adressing review suggestions for Version 1.0.0 #9

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Felix-Kummer commented Aug 13, 2024

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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		--mosaic_visualization = '[boolean]'
		--pyramid_visualization = '[boolean]'

		--save_ard = '[boolean]'
		--save_tsa = '[boolean]'

Adressing review suggestions for Version 1.0.0 #9

Adressing review suggestions for Version 1.0.0 #9

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Felix-Kummer commented Aug 13, 2024

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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mashehu Nov 26, 2024

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github-actions bot commented Aug 13, 2024 •

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