fix: `NEXTFLOW_RUN` to ensure Nextflow Tower and Hasta config compatibility by beatrizsavinhas · Pull Request #27 · Clinical-Genomics/oncoflow

beatrizsavinhas · 2026-10-07T11:42:28Z

Closes https://github.com/Clinical-Genomics/MTP-oncoflow/issues/152.
Closes https://github.com/Clinical-Genomics/MTP-oncoflow/issues/140.

See notes on issue above for more detailed information about the errors that these changes address.

Verified by test_run_v_3_0_0_with_tower.

Changed

Logic for child environment generation in NEXTFLOW_RUN module to reset environment variables that are incompatible with nested runs of child pipelines through Tower and set NXF_WORK for the child pipeline to ensure compatibility with the hasta config.
- Only specific problematic Nextflow variables are now reset instead of the previous approach of reseting all variables except a set that needed to be propagated.
- Tower related environment variables that are incompatible with child runs are now also reset.
- NXF_WORK is set to ${cache_path}/work to ensure the Java tmp dir is correctly set as per the hasta config and in accordance to the cache cleaning logic of the NEXTFLOW_RUN module.

…ion" This reverts commit c023e4a, reversing changes made to 1841034.

…d to test.

github-actions · 2026-10-07T11:43:50Z

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

Posted for pipeline commit 43cdb8e

+| ✅ 162 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  24 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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 CHANGELOG.md: ## v1.0.0dev - [unreleased replace with date on release ]
pipeline_todos - TODO string in README.md: TODO nf-core:
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: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
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 main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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 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 usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
schema_lint - Parameter input not found in schema

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-oncoflow_logo_light.png
files_exist - File is ignored: docs/images/nf-core-oncoflow_logo_light.png
files_exist - File is ignored: docs/images/nf-core-oncoflow_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: tests/default.config
files_exist - File is ignored: tests/default.nf.test
files_exist - File is ignored: CODE_OF_CONDUCT.md
nextflow_config - Config variable ignored: params.input
files_unchanged - File does not exist: 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/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File does not exist: assets/nf-core-oncoflow_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-oncoflow_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-oncoflow_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 - actions_awstest
actions_awsfulltest - actions_awsfulltest
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/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/pr-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_full.config
files_exist - File found: docs/CONTRIBUTING.md
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: 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-oncoflow_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/WorkflowOncoflow.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: 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 Clinical-Genomics/
nextflow_config - Config manifest.homePage began with https://github.com/Clinical-Genomics/
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.oncoanalyser_create_stub_placeholders= false
nextflow_config - Config default value correct: params.oncoanalyser_genome= GRCh38_hmf
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/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 - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/sendmail_template.txt 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 Nextflow minimum version badge matched config. Badge: 26.04.0, Config: 26.04.0
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_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: update_changelog.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: conventional_pr_title.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: add_pr_checklist_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting.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.
modules_config - CREATE_ONCOANALYSER_PARAMS_FILE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ONCOREFINER_PARAMS_FILE 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: 4.1.0
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 4.1.0
Run at 2026-10-12 13:57:29

…g of the cache.

kristinebilgrav

Looks good to me! Great 🚀

beatrizsavinhas added 30 commits September 2, 2026 16:14

Add run name to NEXTFLOW_RUN

c9a7620

Add val_case_id to child pipeline calls

9beb312

Update module test.

1841034

Use task.workflowId for log file name

7e588d6

Apply Mahesh's fix.

4c59cf3

Merge branch 'workflowid-tower-fix' into add-tower-configuration

c023e4a

Remove logic for config file propagation.

ae943ad

Apply tower fix from nf-cascade.

fca07a2

Update oncorefiner revision in test profile.

7201ab1

Update default test snapshot.

72f38e0

Update changelog.

7645600

Merge branch 'update-oncorefiner-version' into apply-tower-fix

c2df068

Add NXF_WORK to nxf_passthrough.

8734b36

Implement minimal environment_variables_to_unset.

55bb4f1

Merge branch 'dev' into test-minimal-tower-fix

363bdc8

Refactor env variable unset logic.

4f519fd

Add export code to inspect environment variables.

0bb808c

Change unset logic.

c5e9349

Comment out all variables except NXF_SCM_FILE.

36be289

Add NXF_IGNORE_RESUME_HISTORY.

46ca987

Merge branch 'add-tower-configuration' into test-minimal-tower-fix

49d4bb9

Revert "Merge branch 'workflowid-tower-fix' into add-tower-configurat…

66552bd

…ion" This reverts commit c023e4a, reversing changes made to 1841034.

Add NXF_CLI

d3d2648

Remove NXF_CLI

d2d23ae

Restore log command.

c84545b

Add NXF_PLUGINS_DEFAULT.

13c25a9

Add TOWER_ACCESS_TOKEN.

d9d3d39

Add tower environment variables.

fbcc702

List all variables mentioned by Seqera. Activate only minimal require…

199f3a9

…d to test.

Code formatting.

1d72284

Revert changes to modules/local/nextflow/run/tests/main.nf.test.

26dd4b5

Remove out of scope formatting changes.

f73fbfc

Clinical-Genomics deleted a comment from github-actions Bot Oct 7, 2026

beatrizsavinhas added 2 commits October 7, 2026 15:55

Update code comments.

352d61d

Update changelog.

a94a038

Clinical-Genomics deleted a comment from github-actions Bot Oct 7, 2026

beatrizsavinhas added 2 commits October 9, 2026 09:45

Test setting NXF_WORK to task.workDir.

47605c0

Update work-dir to cache_path, to match the expected path for cleanin…

6512d8c

…g of the cache.

Clinical-Genomics deleted a comment from github-actions Bot Oct 9, 2026

beatrizsavinhas added 8 commits October 9, 2026 14:11

Add comment on work-dir setup.

2c580b2

Formatting.

bd2ea57

Add NXF_WORK fix.

996c75f

Remove -work-dir option.

dc18b49

Update code comment on setting NXF_WORK.

dcb54ca

Update syntax for setting NXF_WORK.

972b8fb

Update syntax for setting NXF_WORK.

89e09e4

Fix bug for setting NXF_WORK.

eafb15e

beatrizsavinhas commented Oct 12, 2026

View reviewed changes

Comment thread modules/local/nextflow/run/main.nf

beatrizsavinhas changed the title ~~fix: NEXTFLOW_RUN to ensure Nextflow Tower compatibility~~ fix: NEXTFLOW_RUN to ensure Nextflow Tower and hasta config compatibility Oct 12, 2026

Update changelog

11c7678

beatrizsavinhas changed the title ~~fix: NEXTFLOW_RUN to ensure Nextflow Tower and hasta config compatibility~~ fix: NEXTFLOW_RUN to ensure Nextflow Tower and Hasta config compatibility Oct 12, 2026

Update changelog.

43cdb8e

beatrizsavinhas marked this pull request as ready for review October 12, 2026 14:14

beatrizsavinhas requested a review from a team as a code owner October 12, 2026 14:14

beatrizsavinhas commented Oct 13, 2026

View reviewed changes

Comment thread modules/local/nextflow/run/main.nf

beatrizsavinhas mentioned this pull request Oct 13, 2026

API error is thrown when running cascade with Tower mahesh-panchal/nf-cascade#8

Closed

kristinebilgrav approved these changes Oct 13, 2026

View reviewed changes

beatrizsavinhas merged commit 2a600de into dev Oct 13, 2026
12 checks passed

beatrizsavinhas deleted the add-tower-fix branch October 13, 2026 13:43

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fix: `NEXTFLOW_RUN` to ensure Nextflow Tower and Hasta config compatibility - #27

fix: `NEXTFLOW_RUN` to ensure Nextflow Tower and Hasta config compatibility#27
beatrizsavinhas merged 54 commits into
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nf-core pipelines lint overall result: Passed ✅ ⚠️

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