Fix download action by KateSakharova · Pull Request #79 · nf-core/seqsubmit

KateSakharova · 2026-06-30T21:10:28Z

No description provided.

github-actions · 2026-06-30T21:12:02Z

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

Posted for pipeline commit 7714799

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

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
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 nextflow.config: Specify any additional parameters here

❔ 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.
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: 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 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 - 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.

Run details

nf-core/tools version 4.0.2
Run at 2026-07-01 20:32:16

ochkalova

That's one small step for man, one giant leap for the seqsubmit
🦸🏻

KateSakharova added 2 commits June 30, 2026 22:09

try to fix download action

bf5e09c

lint

8b64e77

test

2c5f597

mberacochea reviewed Jul 1, 2026

View reviewed changes

Comment thread .github/workflows/download_pipeline.yml

mberacochea reviewed Jul 1, 2026

View reviewed changes

Comment thread .github/workflows/download_pipeline.yml Outdated

KateSakharova and others added 4 commits July 1, 2026 15:05

add credentials

587d438

test

e294469

fix folder creation in stub of GENOME_UPLOAD module

fa3c249

fix branch definition for download_pipeline.yml

4d622f2

ochkalova approved these changes Jul 1, 2026

View reviewed changes

ochkalova added 3 commits July 1, 2026 18:01

clean up ENA_WEBIN and ENA_WEBIN_PASSWORD names usage

c9d5b8a

create empty file in COUNT_RNA stub

c6a1fbe

stricten empty file expectations for stub mode

eab0de8

KateSakharova marked this pull request as ready for review July 1, 2026 20:11

ochkalova and others added 2 commits July 1, 2026 21:14

fix line index for 1 line file

27b7a4b

ready to merge

7714799

KateSakharova merged commit 327cee7 into dev Jul 1, 2026
20 checks passed

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Uh oh!

Fix download action#79

Fix download action#79
KateSakharova merged 12 commits into
devfrom
1.0.0

KateSakharova commented Jun 30, 2026

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github-actions Bot commented Jun 30, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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KateSakharova commented Jun 30, 2026

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github-actions Bot commented Jun 30, 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: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions Bot commented Jun 30, 2026 •

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