Add tests, use ena-webin-cli handler, refactor modules.conf and update docs by ochkalova · Pull Request #39 · nf-core/seqsubmit

ochkalova · 2026-03-19T10:03:47Z

Features:

replace ena-webin-cli with ena-webin-cli handler
added webin-cli.jar download to reuse it for every upload
webin-cli-wrapper outputs TSV with accessions which resolves Output the list of assigned accessions after pipeline execution #31
FASTAVALIDATOR step added to genomesubmit (previously we only validated fasta in assemblysubmit)

Tests:

multiple tests added along with snapshots and profiles to test --mode mag and --mode metagenomic_assembly, test data pushed to nf-datasets
more info about tests Fix and improve tests for genome and assembly submission workflows #32 (comment)

Bug fixes:

added triggers to only download DBs if there are data to process and no local DB provided,
create output folder for metadata CSV/TSV if it doesn't exist,
resolved OUT_OF_MEM problem in webin-cli-wrapper,
path in metadata CSV/TSV leading to http locations for remote files
solves missing secrets issue Add Github secrets to be able to run nf-tests in GitHub CI #45
solves problem with nf-tests on GitHub actions Add Github secrets to be able to run nf-tests in GitHub CI #45

Other:

massive docs update
refactor modules.config and clean up published results
WEBIN_ACCOUNT renamed to ENA_WEBIN, WEBIN_PASSWORD to ENA_WEBIN_PASSWORD

PR checklist

…vided

…nalyse

… to analyse

…kflow

…-wrapper

nf-core-bot · 2026-03-19T10:04:19Z

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 · 2026-03-19T10:05:39Z

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

Posted for pipeline commit b100a7d

+| ✅ 251 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  15 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 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
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 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
nextflow_config - Config default value correct: params.webin_cli_version= 9.0.3
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_rna_presence.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
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_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_one_contig.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/mag_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.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/mag_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_complete_metadata.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 - FASTAVALIDATOR found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_ADDNAMES_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FASTA_FOR_CATPACK found in conf/modules.config and Nextflow scripts.
modules_config - BARRNAP found in conf/modules.config and Nextflow scripts.
modules_config - TRNASCANSE found in conf/modules.config and Nextflow scripts.
modules_config - COUNT_RNA found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_DATABASEDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_CONTIG 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_WRAPPER found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_ASSEMBLY_MANIFEST found in conf/modules.config and Nextflow scripts.
modules_config - ENA_WEBIN_CLI_DOWNLOAD 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-03-30 09:16:24

…es with unstable content

…sheet

vagkaratzas

Please don't break/remove template stuff now, because you will regret later during new nf-core tools releases, with template merge PRs :D

Left some comments (will leave some more).

Also, if you haven't already done that, before the first release, we will need the def toolCitationText() and def toolBibliographyText() functions of subworkflows/local/utils_nfcore_seqsubmit_pipeline filled with actual citations data (see proteinfamilies pipeline on how to do this).

conf/modules.config

docs/output.md

modules/local/count_rna/tests/data/ecoli.stats

docs/output.md

CITATIONS.md

workflows/genomesubmit.nf

mberacochea

Thanks @ochkalova ... I've left some comments!

modules/nf-core/multiqc/main.nf

subworkflows/nf-core/fasta_classify_catpack/main.nf

workflows/assemblysubmit.nf

workflows/genomesubmit.nf

nextflow.config

vagkaratzas

Alright for me for now. I guess it's better to have the end-to-end snapshots on a subsequent PR (+ some of the other Issues on the standby). I'd recommend 1 PR per 1 issue ;)

vagkaratzas · 2026-03-27T11:26:37Z

Alright for me for now. I guess it's better to have the end-to-end snapshots on a subsequent PR (+ some of the other Issues on the standby). I'd recommend 1 PR per 1 issue ;)

Oh the snapshots are there, but guess some extra files require to be in the .nftignore to make them stable.

vagkaratzas · 2026-03-27T11:30:27Z

Alright for me for now. I guess it's better to have the end-to-end snapshots on a subsequent PR (+ some of the other Issues on the standby). I'd recommend 1 PR per 1 issue ;)

Oh the snapshots are there, but guess some extra files require to be in the .nftignore to make them stable.

For example, since you changed this path in multiqc module config:
path: { "${params.outdir}/${params.mode}/multiqc" },
You will have to add all mode paths to multiqc.log in the .nftignore.

ochkalova · 2026-03-27T12:17:10Z

For example, since you changed this path in multiqc module config:
path: { "${params.outdir}/${params.mode}/multiqc" },
You will have to add all mode paths to multiqc.log in the .nftignore.

Well, I reverted it back to path: { "${params.outdir}/multiqc" }, because it's not mode specific thingy. But multiqc files are already in the snapshots. Snapshots have to be updated 🔨

…lt test.config

Martin is on AL and I had his verbal approval. Also he planned to do corrections in another branch anyway, so I'll dismiss his review for now

KateSakharova and others added 20 commits March 12, 2026 14:50

replace upload with ena-webin-handler

ce31ec7

additions

952ab91

add condition for manifest parsing

e2709e1

rename

0453f2e

Merge remote-tracking branch 'origin/dev' into add_tests

7514d0a

refactor and add check to only download CAT_db if local db is not pro…

931fc86

…vided

add possible fna extension to schemas because we can handle it

f72c32e

patch genome_evaluation to only download db if there are genomes to a…

c599e65

…nalyse

patch fasta_classify_catpack to only download db if there are genomes…

8f52a6c

… to analyse

add FASTAVALIDATOR to check fasta file formatting in GENOMESUBMIT wor…

81dbeb2

…kflow

include FASTAVALIDATOR step to genomesubmit

76498c2

add more published results to modules.conf

6264ee5

add tests for genomesubmit in --mode mag

f6eb677

update methods.md

2ae8f95

update container for webin-cli-wrapper

d422d96

fix typo

201d0ff

add output for accession TSV and update meta description to webin-cli…

1ca99b3

…-wrapper

add test with invalid assembly

b612148

append mag_ to all samplesheets for genomesubmit testing for convenience

6a38731

add tests for assemblysubmit workflow

9e4f980

ochkalova changed the base branch from feature/genome-submission to dev March 19, 2026 11:28

ochkalova added 7 commits March 19, 2026 14:45

create output dir for metadata file if it doesn't exist

75de363

push test data and samplesheets to nf-core/test-datasets

f9bd3d4

add mode-specific test tags, update .nftignore to exclude results fil…

57f22b8

…es with unstable content

update usage doc

d0b47ea

add more tests

c3757d8

add snapshots for tests

ef79beb

pdate container for webin-cli-wrapper

4fc0b10

ochkalova added 3 commits March 25, 2026 15:42

Merge branch 'dev' into add_tests

f7adda8

fixes in tests, snapshot updates

797e019

add notes to readme to ensure expected order of columns in the sample…

87b473a

…sheet

ochkalova requested review from mberacochea and vagkaratzas March 26, 2026 10:43

vagkaratzas requested changes Mar 26, 2026

View reviewed changes

vagkaratzas reviewed Mar 26, 2026

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mberacochea reviewed Mar 26, 2026

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mberacochea previously requested changes Mar 26, 2026

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ochkalova added 2 commits March 26, 2026 15:43

use splitCsv for coverage file parsing

05919f2

apply vangelis linter

25b3d8d

ochkalova requested review from mberacochea and vagkaratzas March 26, 2026 18:36

vagkaratzas approved these changes Mar 27, 2026

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add fallback publishDir and explicitly disable publishing where needed

962acb0

ochkalova added 5 commits March 27, 2026 12:46

update snapshots

e881c0a

add secrets export in github actions

9a17eca

reduce memory allocation in conf files to 12GB for github actions

56fd07f

clean up tests, make test_mag_multiple_bins_missing_metadata.nf defau…

861b92a

…lt test.config

delete slow and greedy nf-test that runs CheckM2

b100a7d

ochkalova merged commit 4a8d78a into dev Mar 30, 2026
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ochkalova deleted the add_tests branch March 30, 2026 09:33

This was referenced Mar 30, 2026

Fix and improve tests for genome and assembly submission workflows #32

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Add Github secrets to be able to run nf-tests in GitHub CI #45

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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vagkaratzas commented Mar 27, 2026

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ochkalova commented Mar 19, 2026 •

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

ochkalova commented Mar 27, 2026 •

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