Release 1.0.0 #7

Felix-Kummer · 2024-07-31T18:50:17Z

PR description

This is the first release of rangeland, a remote sensing pipeline for trend analysis in grasslands.
Rangeland is the first remote sensing pipeline in nf-core and, thus, deviates from most nf-core pipelines.

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!
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).

…core labels

(e.g. nf-core github actions)

Important! Template update for nf-core/tools v2.14.1

github-actions · 2024-07-31T18:51:43Z

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

Posted for pipeline commit 7c9e49d

+| ✅ 205 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

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 manifest.version does not contain dev for release: 1.0.0
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
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-20 12:08:12

mashehu

see #8 (review)

nictru · 2024-08-05T10:28:44Z

Added my thoughts #8 (review)

…essing results, some minor adjustments in the docs.

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

Adressing review suggestions for Version 1.0.0

…into dev

Adressing more reviewer comments for 1.0.0

Disabled publishing of version.yml in visualization processes

Template update for nf-core/tools version 3.1.1

jfy133 · 2025-01-06T09:22:23Z

workflows/rangeland.nf

+    }
+
+    data.ifEmpty {
+        error "No directories found!"


I would maybe make this more informative.

Suggested change

error "No directories found!"

error "[nf-core/rangeland] ERROR: No directories found in input tar file!"

Or similar

jfy133 · 2025-01-06T09:24:02Z

My approval still stands!

mashehu

Some last comment over at #8 but good to go otherwise

Addressed final reviewer suggestion for version 1.0.0

nf-core-bot and others added 22 commits December 19, 2023 19:47

Template update for nf-core/tools version 2.11

4475b7e

Template update for nf-core/tools version 2.11.1

a9012e8

Moved to a more stable version of FORCE

30d36cb

Fixed publishDir for visualization processes

9beb427

Template update for nf-core/tools version 2.12

d760cc7

Template update for nf-core/tools version 2.13

51a4fa5

Added version number to nf-validation plugin

9dc069b

Template update for nf-core/tools version 2.13.1

4790c2d

Template update for nf-core/tools version 2.14.0

dd9e3da

Template update for nf-core/tools version 2.14.1

d6e1398

Removed unnecessary resource requests in modules.conf in favor of nf-…

841399d

…core labels

fixed docker test failures in certain situations

8c1c9d9

(e.g. nf-core github actions)

Ensured that remaining tests run after a single test failure

6fb5757

Merge branch 'dev' into nf-core-template-merge-2.14.1

edf0b33

Fixed indents in merge scripts

9b17ae7

Merge pull request #6 from nf-core/nf-core-template-merge-2.14.1

4ff325a

Important! Template update for nf-core/tools v2.14.1

Added appropriate raster comparisons for trend tif's to test.R

665e862

Increased robustness of test profile against FORCE-related flakiness

b4e8152

Removed only_tile parameter

f292928

Added new options for higher level processing and visualization.

52c93c9

Added test_full profile

a4d297f

bumped version to 1.0.0

b896dda

Felix-Kummer requested a review from jfy133 July 31, 2024 19:42

mashehu requested changes Aug 5, 2024

View reviewed changes

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 mentioned this pull request Aug 13, 2024

Adressing review suggestions for Version 1.0.0 #9

Merged

Felix-Kummer and others added 5 commits November 26, 2024 14:13

Updated nf-core workflows and modules

ba1d17f

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

Merge pull request #9 from CRC-FONDA/dev

caee766

Adressing review suggestions for Version 1.0.0

mashehu approved these changes Nov 26, 2024

View reviewed changes

nf-core-bot and others added 8 commits December 12, 2024 11:25

Template update for nf-core/tools version 3.1.0

edeae16

Aligned Nextflow files with new language-server formatter

b877f51

Added diagram

7b6d06b

Fixed minor issues in README.md

3a5211c

Fixed minor issues in schema

8f17143

Removed some empty lines

4875e12

Merge branch 'dev' of https://github.com/CRC-FONDA/nf-core-rangeland …

e0377eb

…into dev

Merge pull request #12 from CRC-FONDA/dev

e90a0d1

Adressing more reviewer comments for 1.0.0

jfy133 approved these changes Dec 16, 2024

View reviewed changes

Felix-Kummer and others added 8 commits December 18, 2024 13:16

Improved infrastructure-independence

a7d7c4c

Merge branch 'nf-core:dev' into dev

ee02655

Disabled publishing of version.yml in visualization processes

c534f93

Merge pull request #13 from CRC-FONDA/dev

7c9e49d

Disabled publishing of version.yml in visualization processes

Template update for nf-core/tools version 3.1.1

ac7a9ce

Merge branch 'TEMPLATE' of https://github.com/nf-core/rangeland into dev

ba66df2

Merge branch 'nf-core:dev' into dev

7fd48d3

Merge pull request #15 from CRC-FONDA/dev

bfabfee

Template update for nf-core/tools version 3.1.1

jfy133 reviewed Jan 6, 2025

View reviewed changes

mashehu approved these changes Jan 16, 2025

View reviewed changes

Addressed final reviewer suggestion for version 1.0.0

b8cb370

Felix-Kummer mentioned this pull request Jan 17, 2025

Addressed final reviewer suggestion for version 1.0.0 #16

Merged

Merge pull request #16 from CRC-FONDA/dev

f802267

Addressed final reviewer suggestion for version 1.0.0

Felix-Kummer merged commit 7c5cb95 into master Jan 17, 2025
14 of 21 checks passed

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Release 1.0.0 #7

Release 1.0.0 #7

Felix-Kummer commented Jul 31, 2024

github-actions bot commented Jul 31, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mashehu left a comment

nictru commented Aug 5, 2024 •

edited

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jfy133 Jan 6, 2025

jfy133 commented Jan 6, 2025

mashehu left a comment

	error "No directories found!"
	error "[nf-core/rangeland] ERROR: No directories found in input tar file!"

Release 1.0.0 #7

Release 1.0.0 #7

Conversation

Felix-Kummer commented Jul 31, 2024

PR description

PR checklist

github-actions bot commented Jul 31, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mashehu left a comment

Choose a reason for hiding this comment

nictru commented Aug 5, 2024 • edited Loading

jfy133 Jan 6, 2025

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jfy133 commented Jan 6, 2025

mashehu left a comment

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github-actions bot commented Jul 31, 2024 •

edited

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

nictru commented Aug 5, 2024 •

edited

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