Feature/studysubmit by timrozday-mgnify · Pull Request #36 · nf-core/seqsubmit

timrozday-mgnify · 2026-03-12T13:57:37Z

Replace registerstudy with new python script that is general to all ENA studies.

For issue: #30

Update from @ochkalova
What was done in this PR:

added script submit_study.py and corresponding module registerstudy
tests and test profiles for registerstudy module
added input parameter --study_metadata, schema updated
removed params library and ena_raw_reads_study_accession used by previous version of registerstudy
added pipeline level tests for modes mags and metagenomic_assemblies that register study
assemblysubmit and genomesubmit updated to use registerstudy
updated docs

Minor changes:

updated test and snapshot for generate_assembly_manifest/tests/main.nf.test‎
nf-utils version changed to latest

TODOs:

add checks and validation for required fields in webin receipt (accession should always present)
might be worth adding --hold-until to pipeline params

…ainer. Removed linkml validation which is more useful for interactive submission.

…e, distinguish from it sing submit_study is for raw-reads rather than assemblies, and remove references to mimicc.

…ript. Also renamed submit_rawreads_study to submit_study

nf-core-bot · 2026-03-12T13:58:13Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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 · 2026-03-12T13:59:20Z

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

Posted for pipeline commit 55373f8

+| ✅ 210 tests passed       |+
#| ❔   7 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  22 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: 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 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_assembly.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_assembly.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_genome.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_genome.config: Give any required params for the test so that command line flags are not needed
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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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 nextflow.config: Specify any additional parameters here
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
local_component_structure - rna_detection.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - genome_evaluation.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
nextflow_config - Config variable ignored: params.input
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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-seqsubmit_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-seqsubmit_logo_light.png
files_exist - File found: docs/images/nf-core-seqsubmit_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: .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-seqsubmit_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/WorkflowSeqsubmit.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 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.rrna_limit= 80.0
nextflow_config - Config default value correct: params.trna_limit= 18.0
nextflow_config - Config default value correct: params.cat_db_download_id= nr
nextflow_config - Config default value correct: params.checkm2_db_zenodo_id= 14897628.0
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/
nextflow_config - Config default value correct: params.upload_tpa= false
nextflow_config - Config default value correct: params.test_upload= true
nextflow_config - Config default value correct: params.upload_force= true
nextflow_config - Config default value correct: params.webincli_submit= true
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.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/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: 25.04.0, Config: 25.04.0
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_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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-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: 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
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 - CATPACK_ADDNAMES_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_UPLOAD found in conf/modules.config and Nextflow scripts.
modules_config - ENA_WEBIN_CLI found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_ASSEMBLY_MANIFEST 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: 3.5.1
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-03-25 14:17:08

vagkaratzas

Left a round of quick-through comments

…o one, trialling sanitizeOutput for test snapshot.

…puts that have been removed previously

ochkalova · 2026-03-24T14:00:47Z

@@ -0,0 +1,774 @@
+#!/usr/bin/env python3
+"""Submit studies to ENA via the Webin drop-box XML submission service.


Sorry about this 100 line docstring, I needed to show somewhere input file examples, because there is a lot of options and they are not documented anywhere. Even infering from the code what format is required is complicated

mberacochea

Thanks @ochkalova .. I gave it a quick read, and left some tiny comments.

I think we should do another round of cleaning, the python script still does stuff that I'm not sure is relevant for this project.

ochkalova

I tried to clean everything a bit, still some things left to do, but looks good enough to merge

vagkaratzas

Getting in shape!

KateSakharova

Great job!

Requested edits cannot be performed in this PR because require merge to more recent branch with bugfixes

timrozday-mgnify added 8 commits March 12, 2026 11:21

Added submit_study script from private repo

6f04dd6

Modified study-submit script to work in mgnify-pipelines-toolkit cont…

c6d80fb

…ainer. Removed linkml validation which is more useful for interactive submission.

Wrote submit_study module based on submit_study python script.

55c3ca3

Renamed files and parameters to align to existing registerstudy modul…

632ef0a

…e, distinguish from it sing submit_study is for raw-reads rather than assemblies, and remove references to mimicc.

Tidied up code

38e74cf

Rename files

3798fa4

Update tests for study_submit

ab5f92d

Replaced REGSTERSTUDY module with new one based on submit_study.py sc…

6f265d8

…ript. Also renamed submit_rawreads_study to submit_study

timrozday-mgnify requested review from KateSakharova and ochkalova March 12, 2026 13:57

Remove pytest from bin

cc840de

KateSakharova requested a review from vagkaratzas March 12, 2026 14:22

vagkaratzas requested changes Mar 12, 2026

View reviewed changes

mberacochea requested changes Mar 13, 2026

View reviewed changes

KateSakharova requested changes Mar 13, 2026

View reviewed changes

timrozday-mgnify added 12 commits March 13, 2026 12:11

In response to PR comments, merged study_submit.py python scripts int…

d2a78b6

…o one, trialling sanitizeOutput for test snapshot.

Update nft-utils to get sanatizeOutputs to work

15a0f7e

Revert test config

7403a3e

Updated tests to run locally

416fa75

Remove duplicate detection functionality from study submit

7e2b7b8

Remove unused code

1e87af7

Move test fixtures to nf-croe test-datasets

ffc4e90

Merge branch 'dev' into feature/studysubmit

d4f7e76

Fix the tests using nf-core test-datasets and removing inputs and out…

3824311

…puts that have been removed previously

Remove references to dataharmonizer

5d0c83e

Remove xml validation from submit study script

fc14c4b

Split e2e tests into seperate files per workflow

7e586c4

timrozday-mgnify requested a review from vagkaratzas March 13, 2026 14:14

timrozday-mgnify requested a review from KateSakharova March 13, 2026 14:14

nf-core linting

d80420b

ochkalova requested changes Mar 13, 2026

View reviewed changes

ochkalova and others added 10 commits March 23, 2026 14:48

remove dead code

0d743f2

add input format examples, do minor simplifications of the code

763caea

update meta.yml for registerstudy

ac77c70

Merge branch 'dev' into feature/studysubmit

875fa9c

refactor and bugfix registerstudy

6ede603

add real test submission for registerstudy in nf-tests

ab305da

update schema

1ddd2b1

revert some minor changes for branch merging later

6026318

update docs

8ac674d

add tests for pipeline with study registration

6eae0bd

ochkalova reviewed Mar 24, 2026

View reviewed changes

ochkalova added 2 commits March 24, 2026 14:27

apply linter

cc29a3e

linter on .gitignore

bbd8305

ochkalova force-pushed the feature/studysubmit branch from cc29a3e to bbd8305 Compare March 24, 2026 14:35

revert to REST API usage

1a82bec

ochkalova self-requested a review March 24, 2026 15:29

mberacochea approved these changes Mar 24, 2026

View reviewed changes

Comment thread bin/submit_study.py

Comment thread modules/local/registerstudy/main.nf Outdated

ochkalova added 2 commits March 25, 2026 10:31

refactor input parsing in submit_study.py

8e98878

update container for mgnify-pipelines-toolkit

217edea

ochkalova approved these changes Mar 25, 2026

View reviewed changes

vagkaratzas previously requested changes Mar 25, 2026

View reviewed changes

Comment thread conf/test_mag_no_study_complete_metadata.config Outdated

Comment thread conf/test_assembly_no_study_complete_metadata.config Outdated

Comment thread modules/local/genome_upload/main.nf

Comment thread tests/assembly_no_study_complete_metadata.nf.test

remove docker.enabled = true from test profiles, update nextflow.config

55373f8

KateSakharova approved these changes Mar 25, 2026

View reviewed changes

ochkalova merged commit 8c3e48d into dev Mar 25, 2026
17 of 24 checks passed

ochkalova deleted the feature/studysubmit branch March 25, 2026 15:06

ochkalova mentioned this pull request Mar 25, 2026

Improve registerstudy module #30

Closed

		@@ -0,0 +1,774 @@
		#!/usr/bin/env python3
		"""Submit studies to ENA via the Webin drop-box XML submission service.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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timrozday-mgnify commented Mar 12, 2026 •

edited by ochkalova

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github-actions Bot commented Mar 12, 2026 •

edited

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

ochkalova Mar 24, 2026 •

edited

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