merge to main pre transfer by nickp60 · Pull Request #35 · nf-core/funcprofiler

nickp60 · 2026-03-25T16:14:26Z

PR checklist

… not

…b issue

…nprofiler

- Remove log file from snapshot check, as it contains timestamps and will always fail

- Same as last commit, remove log and biom files from snapshot check (they are not stable)

Improve humann tests

- Add missing schema to allOf - Run 'nf-core pipelines lint --fix files_unchanged' to fix linting

github-actions · 2026-04-10T13:09:52Z

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

Posted for pipeline commit 8aa5eb9

+| ✅ 210 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  53 tests had warnings |!

Details

❗ 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: Include a figure that guides the user through the major workflow steps. Many nf-core
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 README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in main.nf: If the module doesn't use arguments ($args), you SHOULD remove:
pipeline_todos - TODO string in meta.yml: # Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: input:Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in main.nf: If the module doesn't use arguments ($args), you SHOULD remove:
pipeline_todos - TODO string in meta.yml: # Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
local_component_structure - concatall.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-funcprofiler_logo_light.png

✅ 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-funcprofiler_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-funcprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-funcprofiler_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: 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-funcprofiler_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/WorkflowFuncprofiler.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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 ends in dev: 1.0.0dev
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.perform_runmerging= true
nextflow_config - Config default value correct: params.run_rgi= false
nextflow_config - Config default value correct: params.run_mifaser= false
nextflow_config - Config default value correct: params.run_eggnogmapper= false
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/funcprofiler/
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/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/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/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/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 - docs/images/nf-core-funcprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcprofiler_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_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_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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 modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - MPAHUMANN4 found in conf/modules.config and Nextflow scripts.
modules_config - HUMANN3 found in conf/modules.config and Nextflow scripts.
modules_config - HUMANN4 found in conf/modules.config and Nextflow scripts.
modules_config - FMHFUNPROFILER found in conf/modules.config and Nextflow scripts.
modules_config - RGI_BWT found in conf/modules.config and Nextflow scripts.
modules_config - EGGNOGMAPPER found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-04-14 07:20:43

miraep8 · 2026-04-11T13:46:05Z

Well, at least it doesn't seem to be failing due to lack of space anymore... but I am a bit flummoxed as to why those snapshots (presumably) match for the docker test but not for the singularity one 🤔

vinisalazar · 2026-04-14T00:58:58Z

@miraep8 I suspect what might be going on is that for some of these outputs, 9/10 times the tool generates a byte-per-byte identical output, but every so often a quirk happens that changes a single character or byte and changes the checksum. Perhaps we could check for file presence rather than checksum for these particular files?

Files generated by mifaser can sometimes not be byte-by-byte identical, failing snapshot checksum assertions. This changes makes it so test assertions check only filename and existence. This should probably be fixed once mifaser is added to nf-core/modules. See #35 for discussion.

Temporary solution until these modules (humann, mifaser) are added to nf-core/modules and their tests are sorted.

🤫

vinisalazar · 2026-04-14T06:40:44Z

@miraep8 you probably already knew that, but separate issue is that sometimes singularity pull is timing out > doesn't generate outputs > they are missing from the snapshot.

Respect the template of ./nextflow.config

nickp60 · 2026-04-14T19:32:05Z

Hmm, I think we've got two separate issues here: singularity humann is returning empty files (with the hash d41d8cd98f00b204e9800998ecf8427e) , and it looks like we have something funny with mifaser as well. I don't think we can just check file presence absence until we understand the differences a bit better.

nickp60 · 2026-04-14T19:34:01Z

There are some snapshot empty files as well, which we will need to fix.

nickp60 · 2026-04-14T20:08:54Z

There are some snapshot empty files as well, which we will need to fix.

Oh some, maybe all, of these are stub outputs so thats expected

vinisalazar · 2026-04-15T00:46:14Z

Hmm, I think we've got two separate issues here: singularity humann is returning empty files (with the hash d41d8cd98f00b204e9800998ecf8427e) , and it looks like we have something funny with mifaser as well. I don't think we can just check file presence absence until we understand the differences a bit better.

Just to confirm, this is happening even when the HUMAnN image is pulled successfully? I thought this was only when the singularity image pull timed out.

The fact that both of the errors are happening in local modules makes me think that perhaps we should try and prioritise adding them to nf-core/modules? That way these problems can be investigated more closely, and separated from the scope of the pipeline.

vinisalazar · 2026-04-15T04:34:20Z

@nickp60 in face of the recent discussions that HUMAnN and mifaser may be generating incorrect/empty files, I may revert some of the commits I did here, if that's okay.

nickp60 and others added 30 commits September 29, 2025 17:58

WIP getting fmhfunprofiler to work

c18bbb9

WIP fmhfunprofiler works on test data

1376799

WIP separate profiling workflows for tools that care about pairing vs…

c2cfad0

… not

WIP humann, sorting db permissions

73ac61a

WIP refactor paired vs concat input

b056e37

WIP database despair

3f57c62

WIP - finished database refactor disaster, debugging missing bowtie2d…

c26362a

…b issue

WIP working mpa/humann

9a0a22a

add humann4 process

96ae4cc

add config for publishdir

9f7ebe4

fix conditional containers and file extensions, add config

f2bc30c

WIP getting tests passing, dealing with uncaught Index error in fmhfu…

f6e0c87

…nprofiler

Merge branch 'dev' of github.com:nickp60/funcprofiler into dev

15baa3d

WIP fixing tests

c561ef5

created HUMANN tests, WIP removing local paths

1238c43

nf-test tests passing

db74011

Use GitHub instead of local filepaths

4258b15

Improve humann3 tests

88e6555

- Remove log file from snapshot check, as it contains timestamps and will always fail

Improve humann4 tests

58d34d8

- Same as last commit, remove log and biom files from snapshot check (they are not stable)

clean up schema, attempt 2 at ignoring log and biom files with nf-test

ecece91

Merge pull request #10 from vinisalazar/dev

98616a8

Improve humann tests

WIP paths, keeping untared dbs

50d33ea

Merge branch 'dev' of github.com:nickp60/funcprofiler into dev

011c71a

clean up snapshot and paths in tests

932ca46

reenable multiqc, fix mpa aliases

ee14595

add mifaser

3327ed4

add humann stub, fix bad test aliases

7b870ef

Add mifaser to subworkflow

3211a40

update gitignore for easier linting

c849ae9

Fix fatal lint errors

a1eefb7

- Add missing schema to allOf - Run 'nf-core pipelines lint --fix files_unchanged' to fix linting

nickp60 added 2 commits April 9, 2026 14:24

Merge branch 'dev' of github.com:nf-core/funcprofiler into dev

5902136

fix .nftignore

68521d5

nickp60 and others added 9 commits April 10, 2026 09:33

bump shards further

b362cf6

attempt to bump storage on runner

341fcd8

try smaller image

797a560

fix typo

1e72710

rollback image

75e6b99

try out small figure again

b8ecd26

new image, tried it out locally first this time :)

4e676aa

make humann3 smaller as well

a93f863

remove volume bump since it curiously increased number of failing jobs

c481794

vinisalazar added 8 commits April 14, 2026 12:27

Add non-deterministic files to .nftignore

a80bc72

Temporary solution until these modules (humann, mifaser) are added to nf-core/modules and their tests are sorted.

Update snapshot

ede7787

🤫

Use correct extension in ignored files

d5a20da

Remove genefamilies from humann/main_v4 stub test

f8666f6

Do the same for humann_v3 test

ef8fe5e

Update snapshots

b6bb063

Increase singularity.pullTimeout

cc3a454

vinisalazar added 2 commits April 14, 2026 17:18

Move singularity.pullTimeout to tests/nextflow.config

0b69293

Respect the template of ./nextflow.config

Add HUMAnN {sample}_reactions.tsv file to .nftignore

8aa5eb9

Provide feedback

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merge to main pre transfer#35

merge to main pre transfer#35
nickp60 wants to merge 178 commits intomainfrom
dev

nickp60 commented Mar 25, 2026

Uh oh!

github-actions bot commented Apr 10, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

miraep8 commented Apr 11, 2026

Uh oh!

vinisalazar commented Apr 14, 2026

Uh oh!

vinisalazar commented Apr 14, 2026

Uh oh!

nickp60 commented Apr 14, 2026

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nickp60 commented Apr 14, 2026

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nickp60 commented Mar 25, 2026

PR checklist

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github-actions bot commented Apr 10, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented Apr 10, 2026 •

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