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FEAT: Add support for sessions.tsv file in BIDS subject folder - #133

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gagnonanthony merged 5 commits into
scilus:devfrom
gagnonanthony:feat/session_tsvs
Nov 6, 2026
Merged

FEAT: Add support for sessions.tsv file in BIDS subject folder#133
gagnonanthony merged 5 commits into
scilus:devfrom
gagnonanthony:feat/session_tsvs

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@gagnonanthony

@gagnonanthony gagnonanthony commented Nov 6, 2026 •
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Current BIDS specification allows participants data to be supplied either in the root-level participants.tsv file or within *sessions.tsv files located within each subject folder. This PR adds support for fetching participants' age in sessions.tsv files if present; otherwise, it defaults to the root-level participants.tsv.

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.

@gagnonanthony gagnonanthony self-assigned this Nov 6, 2026
@gagnonanthony gagnonanthony added the enhancement New feature or request label Nov 6, 2026
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f532370

+| ✅ 132 tests passed       |+
#| ❔  39 tests were ignored |#
!| ❗  21 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_unchanged - LICENSE does not match the template
  • 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_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: //Add all required assertions to verify the test output.
  • 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.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: define inputs of the process here. Example:
  • pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
  • 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 base.config: Customise requirements for specific processes.
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/scilus/sf_pediatric/main/nextflow_schema.json or https://raw.githubusercontent.com/scilus/sf_pediatric/master/nextflow_schema.json.
    Found https://raw.githubusercontent.com/scilus/sf-pediatric/master/nextflow_schema.json
  • 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
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • files_exist - File is ignored: conf/test_full.config
  • nextflow_config - nextflow_config
  • nf_test_content - 'tests/gpu.nf.test' checking ignored
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .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.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 does not exist: assets/nf-core-sf_pediatric_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-sf_pediatric_logo_light.png
  • files_unchanged - File does not exist: 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
  • schema_params - schema_params
  • multiqc_config - multiqc_config
  • container_configs - container_configs

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.1
  • Run at 2026-11-06 17:02:49

@gagnonanthony gagnonanthony mentioned this pull request Nov 6, 2026
Merged
@gagnonanthony
gagnonanthony merged commit 0c976bc into scilus:dev Nov 6, 2026
13 checks passed
@gagnonanthony
gagnonanthony deleted the feat/session_tsvs branch November 6, 2026 18:23
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