[Do not merge!] Pseudo PR for first release #11

mashehu · 2025-09-30T07:37:59Z

Do not merge! This is a PR of dev compared to the TEMPLATE branch for whole-pipeline reviewing purposes. Changes should be made to dev and this PR should not be merged! The actual release PR is at

github-actions · 2025-09-30T07:39:35Z

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

Posted for pipeline commit 3e39d97

+| ✅ 191 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ 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: If applicable, make list of people who have also contributed
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
local_component_structure - utils.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - spaceranger.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/multiqc_config.yml
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-sopa_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sopa_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sopa_logo_dark.png
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: .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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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-sopa_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-sopa_logo_light.png
files_exist - File found: docs/images/nf-core-sopa_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: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
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 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-sopa_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/WorkflowSopa.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.spaceranger_reference= https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz
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.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/baysor.nf.test' contains outdir parameter
nf_test_content - 'tests/baysor.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/baysor.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/cellpose.nf.test' contains outdir parameter
nf_test_content - 'tests/cellpose.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/cellpose.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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 - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.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: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) 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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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.
base_config - PATCH_SEGMENTATION_PROSEG found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SPACERANGER_COUNT 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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-10-02 15:46:45

mashehu

first part of my review

assets/schema_input.json

conf/base.config

conf/test.config

conf/test_baysor.config

docs/output.md

docs/usage.md

modules/local/annotation/environment.yml

modules/local/annotation/main.nf

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

quentinblampey · 2025-09-30T10:32:36Z

Thanks @mashehu for this first review, I updated it accordingly

Just one question regarding your other comment on the original PR:

When doing the change you suggested about the containerOption, I now have this CI error again. It's because for cellpose (one specific segmentation tool, not always used) I need to have permission for its cache directory. I followed this nf-core docs to fix this (see cellpose conf here)

Do you have a solution for it?

mashehu

went through the rest.

modules need to be split
more documentation needs to be moved over to nf-core
nf-core pipelines lint error need to be fixed
nextflow_schema.json is not valid (please use nf-core schema build to edit it in the future)

docs/usage.md

mashehu · 2025-10-02T12:31:34Z

docs/usage.md

+
+## Sopa parameters
+
+You'll also need to choose some Sopa parameters that you'll provide to Nextflow via the `-params-file` option. You can find existing Sopa parameter files [here](https://github.com/gustaveroussy/sopa/tree/main/workflow/config), and follow the [corresponding README instructions](https://github.com/gustaveroussy/sopa/blob/main/workflow/config/README.md) of to get your `-params-file` argument.


sorry, but we having parameter files linked in an external repo is not really the nf-core way. we prefer to have everything nicely bundled together to avoid version mismatches and keep things reusable.

It's possible to provide all the params directly in the command line, but since there are many parameters I just recommend some "presets" to get started, but it's not mandatory to use these
I think the main problem comes from the parameters nested hierarchy, which doesn't show up on the instruction section of sopa on the nf-core website, although they are documented on the nextflow schema
What's your suggestion?

mashehu · 2025-10-02T12:49:12Z

subworkflows/local/utils_nfcore_sopa_pipeline/main.nf

+    def TRANSCRIPT_BASED_METHODS = ['proseg', 'baysor', 'comseg']
+    def STAINING_BASED_METHODS = ['stardist', 'cellpose']


if you put this as enums in your nextflow_schema.json you can skip this

I already list the possible options in the nextflow_schema, but here I want to check more complex logic, like here
I don't know how to do such check with a schema, do you know if it's possible?

mashehu · 2025-10-02T12:49:25Z

subworkflows/local/utils_nfcore_sopa_pipeline/main.nf

+    assert params.read instanceof Map && params.read.containsKey('technology') : "Provide a 'read.technology' key"
+    assert params.containsKey('segmentation') : "Provide a 'segmentation' section"
+
+    // backward compatibility


do you need this for a 1.0.0 release?

anyway you can also do deprecation with the nextflow_schema.json

It can be useful for Sopa users who were using Snakemake and want to move to nf-core/sopa
They could keep the same parameters and it should work, even though their parameters are one year old

Concerning the schema: is it also possible to handle the deprecation logic as in here? Again, I don't know how to update other parameters of the config directly based on the schema

tests/README.md

modules/local/explorer_raw/environment.yml

…he fly

quentinblampey · 2025-10-02T15:47:20Z

Thanks @mashehu for the second round of review!

I split the modules as requested and started adding more docs, but I still have a few questions (see my answer to your review above)

Also, when running nf-core pipelines lint, I don’t see any error - I’m using nf-core version 3.3.2. Which error do you see?

Regarding the schema, what’s the right command line to check that it’s valid? I tried nf-core pipelines schema lint and also received a “schema looks valid” result...

mashehu · 2025-10-06T08:17:00Z

sorry, looks like I linted the wrong version, all good there now concerning linting errors 👍🏻

quentinblampey added 30 commits February 27, 2025 13:58

template repo

96e7091

update schema

cf67583

try running toy dataset

2299ee5

wip

528435d

cellpose is running

8d2cb5e

minor cleanup / test

754e2ec

start using meta

68fa9df

working v0

8fbf215

move cellpose to a subworkflow

64280a4

add baysor

6a1bcb8

make logic between cellpose and baysor

43c7954

can use --config and remove hardcoded publishdir

111c9a7

use label process

fc592eb

minor readme update

7e63060

add conda env files

9d8db7f

fix conda env for cellpose

f4cf634

fix inputs validation (configfile)

7bd5177

clean versions + right explorer outputs

330b2de

add jeffquinnmsk/sopa container

d8166c5

remove image for baysor

a4b9075

try c51 config

e2cab8c

add slurm profile

a9c9918

try validation path

8b1a841

try symlink

4dcaa63

use symlink

0965bc7

publish at the end

8aa086d

use publish dir mode copy

26c2a82

re-run baysor with process_high

99c18de

terminate config

a286369

try errorStrategy = 'ignore'

a00cca6

quentinblampey added 8 commits August 1, 2025 15:32

baysor threads + allow symlink for xenium raw files

4759bc8

fix ro-crate

98511fc

re-run snapshots with fluo annotation

6ea2d56

add tangram to the tests

b943312

update snapshots

cf60411

minor snapshot fix

02e1d7e

add comseg support

1b2d166

singularity on disk large, and disable conda

e0a0084

mashehu commented Sep 30, 2025

View reviewed changes

quentinblampey and others added 6 commits September 30, 2025 10:13

update snapshots and minor fixes

a380894

update regarding mashehu review

5d052ee

Update conf/test.config

bcd298c

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

Update conf/base.config

931a75b

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

Update conf/test_baysor.config

e50c405

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

minor cleanup: comment in test configs

59f8b51

quentinblampey added 8 commits September 30, 2025 15:13

revert docker options

a4d1204

try containerOptions only for docker

c805c80

try make singularity writable

e42156e

try to specify the cellpose cache location

147b35e

try setting cellpose cache in cwd and give more precise proseg inputs

e4ded39

try using TMPDIR

06dbdc3

try containall option for singularity

044bf8f

try export celpose cache loc in process

ed0659b

mashehu commented Oct 2, 2025

View reviewed changes

quentinblampey added 2 commits October 2, 2025 17:33

split modules and start answer to the review

d83d49c

point to another dummy input for the tests as dataset is created on t…

3e39d97

…he fly


		## Sopa parameters

		You'll also need to choose some Sopa parameters that you'll provide to Nextflow via the `-params-file` option. You can find existing Sopa parameter files [here](https://github.com/gustaveroussy/sopa/tree/main/workflow/config), and follow the [corresponding README instructions](https://github.com/gustaveroussy/sopa/blob/main/workflow/config/README.md) of to get your `-params-file` argument.

		def TRANSCRIPT_BASED_METHODS = ['proseg', 'baysor', 'comseg']
		def STAINING_BASED_METHODS = ['stardist', 'cellpose']

[Do not merge!] Pseudo PR for first release #11

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[Do not merge!] Pseudo PR for first release #11

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mashehu commented Sep 30, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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

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