Merge dev into main by gagnonanthony · Pull Request #111 · scilus/sf-pediatric

gagnonanthony · 2026-02-10T02:21:20Z

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!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core pipelines lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
Documentation has been updated according to your changes
CHANGELOG.md is updated.

* remove redundant shell parameters for frf fitting * improve validation of participant_label parameter * clarify parameters for frf and fodf_min_shell_value * add checks for shell selection for both DTI and fODF

gagnonanthony · 2026-02-10T02:22:30Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2026-02-10T02:30:20Z

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

Posted for pipeline commit e0db64a

+| ✅ 335 tests passed       |+
#| ❔  30 tests were ignored |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - Config manifest.version should end in dev: 0.2.2
readme - README did not have a Nextflow minimum version badge.
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_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-sf-pediatric_logo_light.png
files_exist - File is ignored: docs/images/nf-core-sf-pediatric_logo_light.png
files_exist - File is ignored: docs/images/nf-core-sf-pediatric_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: tests/default.nf.test
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-sf-pediatric_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sf-pediatric_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sf-pediatric_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sf-pediatric/sf-pediatric/.github/workflows/awstest.yml
template_strings - template_strings
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: 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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
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-sf-pediatric_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/WorkflowSf-pediatric.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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.method= recon-all-clinical
nextflow_config - Config default value correct: params.cerebnet= false
nextflow_config - Config default value correct: params.hypvinn= false
nextflow_config - Config default value correct: params.acq3T= true
nextflow_config - Config default value correct: params.mcribs_fastcollision= false
nextflow_config - Config default value correct: params.mcribs_nopialoutside= false
nextflow_config - Config default value correct: params.mcribs_seed= 1234.0
nextflow_config - Config default value correct: params.preproc_run_denoising= true
nextflow_config - Config default value correct: params.preproc_run_N4= true
nextflow_config - Config default value correct: params.preproc_run_resampling= true
nextflow_config - Config default value correct: params.preproc_run_synthstrip= true
nextflow_config - Config default value correct: params.preproc_run_ants_bet= false
nextflow_config - Config default value correct: params.preproc_run_crop= true
nextflow_config - Config default value correct: params.t1_denoise_number_of_coils= 1
nextflow_config - Config default value correct: params.t1_bias_bspline_knot_per_voxel= 8.0
nextflow_config - Config default value correct: params.t1_bias_shrink_factor= 4
nextflow_config - Config default value correct: params.t1_resample_voxel_size= 1
nextflow_config - Config default value correct: params.t1_resample_interp= lin
nextflow_config - Config default value correct: params.t1_synthstrip_border= 1
nextflow_config - Config default value correct: params.t1_synthstrip_nocsf= false
nextflow_config - Config default value correct: params.t2_denoise_number_of_coils= 1
nextflow_config - Config default value correct: params.t2_bias_bspline_knot_per_voxel= 8.0
nextflow_config - Config default value correct: params.t2_bias_shrink_factor= 4
nextflow_config - Config default value correct: params.t2_resample_voxel_size= 1
nextflow_config - Config default value correct: params.t2_resample_interp= lin
nextflow_config - Config default value correct: params.t2_synthstrip_border= 1
nextflow_config - Config default value correct: params.t2_synthstrip_nocsf= false
nextflow_config - Config default value correct: params.coreg_dimensionality= 3
nextflow_config - Config default value correct: params.coreg_transform= a
nextflow_config - Config default value correct: params.coreg_quick= false
nextflow_config - Config default value correct: params.skip_dwi_preprocessing= false
nextflow_config - Config default value correct: params.dwi_b0_threshold= 20
nextflow_config - Config default value correct: params.dwi_shell_tolerance= 50
nextflow_config - Config default value correct: params.preproc_dwi_run_denoising= true
nextflow_config - Config default value correct: params.dwi_denoise_patch_size= 7
nextflow_config - Config default value correct: params.preproc_dwi_run_degibbs= false
nextflow_config - Config default value correct: params.topup_eddy_run_topup= true
nextflow_config - Config default value correct: params.dwi_susceptibility_config_file= b02b0.cnf
nextflow_config - Config default value correct: params.dwi_susceptibility_output_prefix= topup_results
nextflow_config - Config default value correct: params.dwi_susceptibility_readout= 0.04
nextflow_config - Config default value correct: params.dwi_susceptibility_encoding_dir= y
nextflow_config - Config default value correct: params.topup_eddy_run_eddy= true
nextflow_config - Config default value correct: params.dwi_motion_and_eddy_command= eddy_cpu
nextflow_config - Config default value correct: params.dwi_motion_and_eddy_bet_f_threshold= 0.16
nextflow_config - Config default value correct: params.dwi_motion_and_eddy_restore_slices= true
nextflow_config - Config default value correct: params.dwi_run_synthstrip= true
nextflow_config - Config default value correct: params.dwi_synthstrip_border= 1
nextflow_config - Config default value correct: params.dwi_synthstrip_nocsf= false
nextflow_config - Config default value correct: params.dwi_bet_f_threshold= 0.16
nextflow_config - Config default value correct: params.preproc_dwi_run_N4= true
nextflow_config - Config default value correct: params.dwi_bias_bspline_knot_per_voxel= 8.0
nextflow_config - Config default value correct: params.dwi_bias_shrink_factor= 4
nextflow_config - Config default value correct: params.dwi_normalize_fa_mask_threshold= 0.4
nextflow_config - Config default value correct: params.preproc_dwi_run_resampling= true
nextflow_config - Config default value correct: params.dwi_resample_voxel_size= 1
nextflow_config - Config default value correct: params.dwi_resample_interp= lin
nextflow_config - Config default value correct: params.dwi_resample_mask_voxel_size= 1
nextflow_config - Config default value correct: params.dwi_resample_mask_interp= nn
nextflow_config - Config default value correct: params.dti_max_shell_value= 1200
nextflow_config - Config default value correct: params.frf_fa= 0.7
nextflow_config - Config default value correct: params.frf_min_fa= 0.5
nextflow_config - Config default value correct: params.frf_nvox_min= 300
nextflow_config - Config default value correct: params.frf_roi_radius= 20
nextflow_config - Config default value correct: params.frf_set_method= ssst
nextflow_config - Config default value correct: params.fodf_min_shell_value= 700
nextflow_config - Config default value correct: params.fodf_sh_order= 8
nextflow_config - Config default value correct: params.fodf_sh_basis= descoteaux07
nextflow_config - Config default value correct: params.fodf_set_method= ssst
nextflow_config - Config default value correct: params.fodf_relative_threshold= 0.1
nextflow_config - Config default value correct: params.fodf_a_factor= 2.0
nextflow_config - Config default value correct: params.fodf_max_fa_threshold= 0.1
nextflow_config - Config default value correct: params.fodf_min_md_threshold= 0.002
nextflow_config - Config default value correct: params.run_pft_tracking= true
nextflow_config - Config default value correct: params.pft_seeding_mask_type= wm
nextflow_config - Config default value correct: params.pft_fa_threshold= 0.2
nextflow_config - Config default value correct: params.pft_random_seed= 1234
nextflow_config - Config default value correct: params.pft_compress= true
nextflow_config - Config default value correct: params.pft_compress_value= 0.2
nextflow_config - Config default value correct: params.pft_algo= prob
nextflow_config - Config default value correct: params.pft_nbr_seeds= 10
nextflow_config - Config default value correct: params.pft_seeding_type= npv
nextflow_config - Config default value correct: params.pft_step= 0.5
nextflow_config - Config default value correct: params.pft_theta= 20.0
nextflow_config - Config default value correct: params.pft_sfthres= 0.1
nextflow_config - Config default value correct: params.pft_sfthres_init= 0.5
nextflow_config - Config default value correct: params.pft_min_len= 20.0
nextflow_config - Config default value correct: params.pft_max_len= 200.0
nextflow_config - Config default value correct: params.pft_particles= 15
nextflow_config - Config default value correct: params.pft_back= 2
nextflow_config - Config default value correct: params.pft_front= 1
nextflow_config - Config default value correct: params.run_local_tracking= true
nextflow_config - Config default value correct: params.local_seeding_mask_type= wm
nextflow_config - Config default value correct: params.local_fa_tracking_mask_threshold= 0.4
nextflow_config - Config default value correct: params.local_fa_seeding_mask_threshold= 0.4
nextflow_config - Config default value correct: params.local_tracking_mask_type= wm
nextflow_config - Config default value correct: params.local_random_seed= 1234
nextflow_config - Config default value correct: params.local_compress= true
nextflow_config - Config default value correct: params.local_compress_value= 0.2
nextflow_config - Config default value correct: params.local_algo= prob
nextflow_config - Config default value correct: params.local_nbr_seeds= 10
nextflow_config - Config default value correct: params.local_seeding_type= npv
nextflow_config - Config default value correct: params.local_step= 0.5
nextflow_config - Config default value correct: params.local_theta= 20.0
nextflow_config - Config default value correct: params.local_sfthres= 0.1
nextflow_config - Config default value correct: params.local_min_len= 20.0
nextflow_config - Config default value correct: params.local_max_len= 200.0
nextflow_config - Config default value correct: params.average_diff_priors= false
nextflow_config - Config default value correct: params.run_noddi= false
nextflow_config - Config default value correct: params.noddi_lambda1= 0.5
nextflow_config - Config default value correct: params.noddi_lambda2= 0.001
nextflow_config - Config default value correct: params.run_freewater= false
nextflow_config - Config default value correct: params.freewater_lambda1= 0.0
nextflow_config - Config default value correct: params.freewater_lambda2= 0.25
nextflow_config - Config default value correct: params.minimal_vote_ratio= 0.5
nextflow_config - Config default value correct: params.outlier_alpha= 0.6
nextflow_config - Config default value correct: params.nb_points= 5
nextflow_config - Config default value correct: params.colormap= jet
nextflow_config - Config default value correct: params.use_hyperplane= false
nextflow_config - Config default value correct: params.use_manhattan= false
nextflow_config - Config default value correct: params.density_weighting= true
nextflow_config - Config default value correct: params.normalize_weights= true
nextflow_config - Config default value correct: params.length_stats= true
nextflow_config - Config default value correct: params.endpoints_stats= true
nextflow_config - Config default value correct: params.means_std= true
nextflow_config - Config default value correct: params.volume= true
nextflow_config - Config default value correct: params.streamline_count= true
nextflow_config - Config default value correct: params.volume_per_labels= true
nextflow_config - Config default value correct: params.mean_std_per_point= true
nextflow_config - Config default value correct: params.labels_transform_dimensionality= 3
nextflow_config - Config default value correct: params.labels_output_suffix= _labels
nextflow_config - Config default value correct: params.labels_interpolation= NearestNeighbor
nextflow_config - Config default value correct: params.labels_output_dtype= int
nextflow_config - Config default value correct: params.run_commit2= true
nextflow_config - Config default value correct: params.commit2_lambda= 0.001
nextflow_config - Config default value correct: params.commit_ball_stick= false
nextflow_config - Config default value correct: params.commit_nbr_dir= 500
nextflow_config - Config default value correct: params.decompose_no_pruning= false
nextflow_config - Config default value correct: params.decompose_no_remove_loops= false
nextflow_config - Config default value correct: params.decompose_no_remove_outliers= false
nextflow_config - Config default value correct: params.decompose_no_remove_curv= false
nextflow_config - Config default value correct: params.decompose_min_len= 20.0
nextflow_config - Config default value correct: params.decompose_max_len= 200.0
nextflow_config - Config default value correct: params.decompose_outlier_threshold= 0.6
nextflow_config - Config default value correct: params.decompose_max_angle= 330.0
nextflow_config - Config default value correct: params.decompose_max_curv= 10.0
nextflow_config - Config default value correct: params.afd_fixel_length_weighting= false
nextflow_config - Config default value correct: params.templateflow_res= 1
nextflow_config - Config default value correct: params.templateflow_home= ./templateflow
nextflow_config - Config default value correct: params.use_template_t2w= false
nextflow_config - Config default value correct: params.tracking= false
nextflow_config - Config default value correct: params.bundling= false
nextflow_config - Config default value correct: params.connectomics= false
nextflow_config - Config default value correct: params.segmentation= 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
nf_test_content - 'tests/chained.nf.test' contains outdir parameter
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' contains outdir parameter
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' contains outdir parameter
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' contains outdir parameter
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chained.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/connectomics.nf.test' contains outdir parameter
nf_test_content - 'tests/connectomics.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/connectomics.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/connectomics.nf.test' contains outdir parameter
nf_test_content - 'tests/connectomics.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/connectomics.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/connectomics.nf.test' contains outdir parameter
nf_test_content - 'tests/connectomics.nf.test' contains outdir parameter
nf_test_content - 'tests/segmentation.nf.test' contains outdir parameter
nf_test_content - 'tests/segmentation.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/segmentation.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/segmentation.nf.test' contains outdir parameter
nf_test_content - 'tests/segmentation.nf.test' contains outdir parameter
nf_test_content - 'tests/bundleseg.nf.test' contains outdir parameter
nf_test_content - 'tests/bundleseg.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bundleseg.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
nf_test_content - 'tests/tracking.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tracking.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
nf_test_content - 'tests/tracking.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tracking.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
nf_test_content - 'tests/tracking.nf.test' contains outdir parameter
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 - LICENSE matches the template
files_unchanged - .github/.dockstore.yml 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
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
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: deploy.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: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.4.1
Run at 2026-02-10 19:27:19

gagnonanthony and others added 2 commits February 9, 2026 21:15

ENH: Improve parameters validation (#110)

fb764ea

* remove redundant shell parameters for frf fitting * improve validation of participant_label parameter * clarify parameters for frf and fodf_min_shell_value * add checks for shell selection for both DTI and fODF

update changelog

f000a04

gagnonanthony self-assigned this Feb 10, 2026

hide some advanced parameters

e0db64a

gagnonanthony merged commit 7573704 into main Feb 11, 2026
17 checks passed

gagnonanthony deleted the dev branch February 11, 2026 01:31

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Merge dev into main#111

Merge dev into main#111
gagnonanthony merged 3 commits intomainfrom
dev

gagnonanthony commented Feb 10, 2026

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github-actions bot commented Feb 10, 2026 •

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gagnonanthony commented Feb 10, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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