Initial release by KateSakharova · Pull Request #72 · nf-core/seqsubmit

KateSakharova · 2026-06-15T14:56:19Z

nf-core/seqsubmit v1.0.0 — Initial Release

This is the first release of nf-core/seqsubmit, a Nextflow pipeline for submitting sequence data to the European Nucleotide Archive (ENA).

What it does:

The pipeline supports four submission modes via dedicated workflows:

mags — Metagenome Assembled Genomes submission (GENOMESUBMIT)
bins — Metagenomic bins submission (GENOMESUBMIT)
metagenomic_assemblies — Assembly submission (ASSEMBLYSUBMIT)
reads — Raw sequencing reads submission (READSUBMIT)

Key features:

Automatic study registration with ENA when no existing study accession is provided
Support for public and private data submissions, including configurable release dates
Coverage calculation from reads when not provided directly (via coverm)
Completeness/contamination estimation and taxonomy inference for MAGs/bins (via CheckM2 and CAT_pack) when metadata is incomplete
Credentials handled securely via Nextflow secrets (ENA_WEBIN, ENA_WEBIN_PASSWORD)
Full nf-core compatibility: runs with conda, Docker, and Singularity

Workflows and modules

READSUBMIT — manifest generation and webin-cli submission for raw reads
ASSEMBLYSUBMIT — manifest generation and webin-cli submission for metagenomic assemblies
GENOMESUBMIT — metadata table generation, genome upload, and webin-cli submission for MAGs/bins
Local modules: REGISTERSTUDY, CREATE_READS_MANIFEST, GENERATE_ASSEMBLY_MANIFEST, GENOME_UPLOAD, ENA_WEBIN_CLI_WRAPPER, and supporting utility modules

docs fixes

…prototype Updated genome submitter prototype

…'t change any behavior of this module.

Add READSUBMIT workflow

* remove study metadata files * remove test files for COUNT_RNA module * replace test files for RENAME_FASTA_FOR_CATPACK module and update snapshots

github-actions · 2026-06-15T14:58:25Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 6690021

+| ✅ 252 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗  15 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.0.0dev
version_consistency - manifest.version was not numeric: 1.0.0dev!
version_consistency - nfcore_yml.version was not numeric: 1.0.0dev!
included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/seqsubmit/seqsubmit/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_
local_component_structure - rna_detection.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - fasta_validation.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
container_configs - container_configs

✅ 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/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/CONTRIBUTING.md
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 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_download_id= 14897628
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.is_private= false
nextflow_config - Config default value correct: params.webincli_mode= submit
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_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/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/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_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/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_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/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_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/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/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_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/reads_paired_end.nf.test' contains outdir parameter
nf_test_content - 'tests/reads_paired_end.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/reads_paired_end.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/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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge 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: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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 - FALINT 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 - CREATE_ASSEMBLY_METADATA_CSV found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_METADATA 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 - REGISTERSTUDY 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: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.0.0dev, nfcore_yml.version = 1.0.0dev

Run details

nf-core/tools version 4.0.2
Run at 2026-06-25 19:25:17

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

update genome_uploader

vagkaratzas and others added 30 commits October 21, 2025 15:42

Kate's stuff copy pasted + pre-commit

d4dd5c3

samplesheet_genomesubmit for test profile

aa16b27

correct fasta pattern and samplesheet path

0982ec8

template bug fix

0ec1e75

config params added to schema json

3b1077f

samplesheet function updated

28e00a1

readme secrets guide, samplesheet fasta path parsing for work dir

d838ca5

more samplesheet prasing

3875f0e

docs fixes

309c8af

more fixes

a81a171

return todo

208a511

Merge pull request #1 from EBI-Metagenomics/fixes

1b6ac57

docs fixes

enum options for mode in config and put back readme TODOs

e9059b9

correctly joining input for ENA_WEBIN_CLI

bcc42b6

correctly quoting ENA credentials in webin cli module

30c374a

warnings fixed

a5ed184

changelog update

c95406f

fix in wording

a7d9185

Merge pull request #2 from EBI-Metagenomics/updated_genome_submitter_…

0321b9a

…prototype Updated genome submitter prototype

remove excessive params

30b87ae

add nf-core module template

ef17f01

first draft of the process

00e7c3b

add wave container

f84bcb1

drop version write for assembly-uploader for now

7ec537d

run pre-commit

05c85f6

pre-commit on assets/samplesheet.csv

5964581

add fasta as input param, add unit test

e55b8ad

remove a comment

d8d3efa

fix lint

b04bef9

ro crate

05286c1

timrozday-mgnify and others added 12 commits May 19, 2026 08:32

Tidy up flags and minor fixes

a9ba936

Remove test_upload argument from CREATE_READS_MANIFEST since it doesn…

852d89e

…'t change any behavior of this module.

Move bin/create_reads_manifest.py to mgnify-pipelines-toolkit

5bde07a

Update mgnify-pipelines-toolkit version to 1.5.1

85541b5

add single quotes for metadata values

b26b07d

update pipeline metromap

486ae28

update snapshots

dd7feec

update containers

acf1ee0

update samplesheet path

40db261

update .nftignore

1d94d7d

Merge pull request #58 from nf-core/feat/readsubmit

c744f44

Add READSUBMIT workflow

Delete test files from the repo and use nf-core datasets instead (#71)

b8cbf9b

* remove study metadata files * remove test files for COUNT_RNA module * replace test files for RENAME_FASTA_FOR_CATPACK module and update snapshots

KateSakharova and others added 17 commits June 19, 2026 14:30

update genome_uploader

573fa95

add private

1b906a4

add to readme

6733125

lint

475509a

lint

6daf3eb

Update README.md

ceaaa43

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

wip fixing tests

84f3cd1

wip fixing tests

17783b6

wip fixing tests

822f48e

fix alias

d4a66e8

update logos

24fb81e

update logos

03ea56d

update logos

1e18a1d

lint

6d5d510

typos

487b9ba

lint

511d3e6

Merge pull request #73 from nf-core/hotfix/genome-upload

6690021

update genome_uploader

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Initial release#72

Initial release#72
KateSakharova wants to merge 247 commits into
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KateSakharova commented Jun 15, 2026 •

edited

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github-actions Bot commented Jun 15, 2026 •

edited

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KateSakharova commented Jun 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Failed ❌

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KateSakharova commented Jun 15, 2026 •

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github-actions Bot commented Jun 15, 2026 •

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`nf-core pipelines lint` overall result: Failed ❌