Release 1.1.0 - Resolution Road #105

FloWuenne · 2025-02-28T21:15:24Z

This PR will update the master branch for the next release 1.1.0 Resolution Road.

PR checklist

Sync dev to master

Co-authored-by: Florian Wuennemann <[email protected]>

Merging template updates, dev version bump after release, module update

Co-authored-by: Florian Wuennemann <[email protected]>

Fixed multiqc report

Mindagap skip

Demo

updated changelog

…n.nf

Prepare release 1.1.0

github-actions · 2025-02-28T21:16:36Z

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

Posted for pipeline commit 0ff57c2

+| ✅ 230 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ 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-molkart_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-molkart_logo_light.png
files_exist - File found: docs/images/nf-core-molkart_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.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 found: ro-crate-metadata.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-molkart_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/WorkflowMolkart.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: 1.1.0
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.segmentation_method= mesmer
nextflow_config - Config default value correct: params.cellpose_diameter= 30
nextflow_config - Config default value correct: params.cellpose_chan= 0
nextflow_config - Config default value correct: params.cellpose_pretrained_model= cyto
nextflow_config - Config default value correct: params.cellpose_flow_threshold= 0.4
nextflow_config - Config default value correct: params.cellpose_edge_exclude= true
nextflow_config - Config default value correct: params.mesmer_image_mpp= 0.138
nextflow_config - Config default value correct: params.mesmer_compartment= whole-cell
nextflow_config - Config default value correct: params.stardist_model= 2D_versatile_fluo
nextflow_config - Config default value correct: params.stardist_n_tiles_x= 3
nextflow_config - Config default value correct: params.stardist_n_tiles_y= 3
nextflow_config - Config default value correct: params.mindagap_boxsize= 3
nextflow_config - Config default value correct: params.mindagap_loopnum= 40
nextflow_config - Config default value correct: params.clahe_cliplimit= 0.01
nextflow_config - Config default value correct: params.clahe_nbins= 256
nextflow_config - Config default value correct: params.clahe_pixel_size= 0.138
nextflow_config - Config default value correct: params.clahe_kernel= 25.0
nextflow_config - Config default value correct: params.mindagap_tilesize= 2144
nextflow_config - Config default value correct: params.clahe_pyramid_tile= 1072
nextflow_config - Config default value correct: params.crop_size_x= 400
nextflow_config - Config default value correct: params.crop_size_y= 400
nextflow_config - Config default value correct: params.crop_amount= 4
nextflow_config - Config default value correct: params.crop_nonzero_fraction= 0.4
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-molkart_logo_light.png matches the template
files_unchanged - docs/images/nf-core-molkart_logo_light.png matches the template
files_unchanged - docs/images/nf-core-molkart_logo_dark.png matches the template
files_unchanged - docs/README.md 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'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - ILASTIK_PIXELCLASSIFICATION found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - MOLKARTQC found in conf/modules.config and Nextflow scripts.
modules_config - MOLKARTQCPNG found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_STACK found in conf/modules.config and Nextflow scripts.
modules_config - MASKFILTER found in conf/modules.config and Nextflow scripts.
modules_config - MINDAGAP_MINDAGAP found in conf/modules.config and Nextflow scripts.
modules_config - MINDAGAP_DUPLICATEFINDER found in conf/modules.config and Nextflow scripts.
modules_config - SPOT2CELL found in conf/modules.config and Nextflow scripts.
modules_config - ILASTIK_PIXELCLASSIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - ILASTIK_MULTICUT found in conf/modules.config and Nextflow scripts.
modules_config - CROPHDF5 found in conf/modules.config and Nextflow scripts.
modules_config - CROPTIFF found in conf/modules.config and Nextflow scripts.
modules_config - TIFFH5CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - CLAHE found in conf/modules.config and Nextflow scripts.
modules_config - STARDIST found in conf/modules.config and Nextflow scripts.
modules_config - DEEPCELL_MESMER found in conf/modules.config and Nextflow scripts.
modules_config - CELLPOSE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ANNDATA 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: 3.2.0
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 3.2.0
Run at 2025-03-04 17:39:09

maxulysse · 2025-03-03T12:57:37Z

you seem to have CI issues, is that planned or normal?

kbestak · 2025-03-03T14:22:24Z

It was not expected, in a template update, I changed the CI and skipped conda only on dev, I opened a PR with the fix: #106

FloWuenne · 2025-03-03T14:22:38Z

you seem to have CI issues, is that planned or normal?

@maxulysse Not planned. Forgot to disable conda for the full pipeline test. Will make fix and add to this PR 👍🏻 !

Exclude conda from all tests.

FloWuenne · 2025-03-03T18:18:33Z

@maxulysse All checks green now ✅ !

CHANGELOG.md

CITATIONS.md

maxulysse · 2025-03-04T08:52:43Z

assets/nf-core-molkart_logo_light.png

Don't you have a logo?

We do have a logo, don't know where that went in the repo @kbestak? Logo can be found here also:
https://github.com/nf-core/logos/tree/master/hexagon-stickers/molkart

maxulysse · 2025-03-04T08:54:41Z

conf/igenomes_ignored.config

you shouldn't need this file.
do you have igenomes in the nf-core features to ignore?

I am guessing this is a remnant from an older template that didn't get removed automatically?

kill it with fire

maxulysse · 2025-03-04T08:55:13Z

docs/images/nf-core-molkart_logo_dark.png

what happened to the logo?

maxulysse · 2025-03-04T08:58:22Z

tests/main.nf.test

nft-utils would make the snapshots both easier and more complete

Can you be a bit more specific here? What exactly from nft-utils would help here. Is that something we can do for the next release or you think it would help for this version?

basically follow this logic:
https://github.com/nf-core/sarek/blob/master/tests/default.nf.test#L1-L41
remove
https://github.com/nf-core/sarek/blob/master/tests/default.nf.test#L22-L24
and
https://github.com/nf-core/sarek/blob/master/tests/default.nf.test#L36-L37

That will capture ALL the files produced by the pipeline
You will need a .nftignorefile such as https://github.com/nf-core/sarek/blob/master/tests/.nftignore
and you adapt the non stable files with its content

maxulysse · 2025-03-04T08:59:05Z

tests/nextflow.config

@@ -4,3 +4,4 @@
 ========================================================================================
 */

+trace.overwrite = true


do you really need that?

@kbestak This was added in this commit? Any idea if it's required?
1590059

maxulysse

Looking good, minor requests

Co-authored-by: Maxime U Garcia <[email protected]>

kbestak and others added 30 commits January 3, 2024 09:31

Merged changes from nf-core template

869656a

Template update for nf-core/tools version 2.12

9a1b00b

Template update for nf-core/tools version 2.13

dfadd43

Merge pull request #58 from nf-core/master

63426b8

Sync dev to master

Template update for nf-core/tools version 2.13.1

fa94b22

Template update for nf-core/tools version 2.14.0

0616ede

Template update for nf-core/tools version 2.14.1

66ff1ed

template_update_2.14.1

1ed382a

template update

708e799

removed leftover view()

b0fc281

fixed modules.json

0c5893e

Update CHANGELOG.md

f6026d5

Co-authored-by: Florian Wuennemann <[email protected]>

removed todo in ci.yml, added singularity test

58fa5b3

removed singularity test

3a408e9

Merge pull request #71 from kbestak/merging-template-updates

a28da2c

Merging template updates, dev version bump after release, module update

Fixed multiqc report

7d35334

updated changelog

1d7e809

Update CHANGELOG.md

372c78b

Co-authored-by: Florian Wuennemann <[email protected]>

removed seqera container for multiqc

07d44b1

mindagap_skip

795acd5

fixed collect_QC

4f14222

added test for skip mindagap

1590059

adapted citations

6dbf1b1

Merge pull request #76 from kbestak/multiqc_report_fix

b5aee86

Fixed multiqc report

Merge pull request #78 from kbestak/mindagap_skip

b12929c

Mindagap skip

added_stardist

43ac414

added test

c7fbb67

added stardist to test config

6e61d61

stardist documentation

52117e1

Merge pull request #2 from kbestak/demo

b3a99a3

Demo

kbestak and others added 8 commits February 27, 2025 14:56

Merge pull request #103 from kbestak/changelog

a5e6a31

updated changelog

lint fix: Moved local modules to individual folders and rename to mai…

c16dd52

…n.nf

Updated CHANGELOG.

4535aee

lint fix: Removed leftover TODOs from template update.

02985e9

Bump version to 1.1.0

5ca42d7

Fix pre-commit formatting.

df7fd4d

Added /main to all local module includes.

d632a0f

Merge pull request #104 from FloWuenne/prepare-release-1.1.0

0f394c5

Prepare release 1.1.0

FloWuenne changed the title ~~Release 1.1.0~~ Release 1.1.0 - Resolution Road Feb 28, 2025

FloWuenne requested a review from maxulysse March 1, 2025 13:25

kbestak added 3 commits March 3, 2025 14:10

updated ci to exlude conda

403ac2c

removed commented conda reference

73b50a2

skipping singularity on dev

419dfbb

kbestak and others added 2 commits March 3, 2025 14:42

returned singularity testing to dev

6e8a6b6

Merge pull request #106 from kbestak/ci_update

9f5ae53

Exclude conda from all tests.

maxulysse reviewed Mar 4, 2025

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what happened to the logo?

maxulysse reviewed Mar 4, 2025

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Update CITATIONS.md

0ff57c2

Co-authored-by: Maxime U Garcia <[email protected]>

lpantano approved these changes Mar 4, 2025

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Release 1.1.0 - Resolution Road #105

Release 1.1.0 - Resolution Road #105

FloWuenne commented Feb 28, 2025

github-actions bot commented Feb 28, 2025 •

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❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Mar 3, 2025

kbestak commented Mar 3, 2025

FloWuenne commented Mar 3, 2025

FloWuenne commented Mar 3, 2025

maxulysse Mar 4, 2025

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maxulysse left a comment

Release 1.1.0 - Resolution Road #105

Are you sure you want to change the base?

Release 1.1.0 - Resolution Road #105

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FloWuenne commented Feb 28, 2025

PR checklist

github-actions bot commented Feb 28, 2025 • edited Loading

nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Mar 3, 2025

kbestak commented Mar 3, 2025

FloWuenne commented Mar 3, 2025

FloWuenne commented Mar 3, 2025

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github-actions bot commented Feb 28, 2025 •

edited

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

FloWuenne Mar 4, 2025 •

edited

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