Release version 1.1.3 #237

heuermh · 2025-01-30T16:30:29Z

PR checklist

bump to 1.2.0dev

update workflow svg

Merging template updates for versions 2.14.0 through 3.1.1

Update nf-core/smoothxg module to version 0.8.0

make parameter `n_haplotypes` null

prepare new release 1.1.3 - marsupial

heuermh · 2025-01-30T16:43:15Z

Attempting to resolve merge conflicts in #238

Resolve merge conflicts

github-actions · 2025-01-30T17:19:31Z

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

Posted for pipeline commit f2b63fe

+| ✅ 235 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
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!
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - pggb.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - odgi_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - community.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-pangenome_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: .editorconfig
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/ci.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-pangenome_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-pangenome_logo_light.png
files_exist - File found: docs/images/nf-core-pangenome_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: 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-pangenome_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/WorkflowPangenome.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: params.input
nextflow_config - Config variable found: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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 does not contain dev for release: 1.1.3
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.wfmash_map_pct_id= 90.0
nextflow_config - Config default value correct: params.wfmash_segment_length= 5000
nextflow_config - Config default value correct: params.wfmash_mash_kmer= 19
nextflow_config - Config default value correct: params.wfmash_mash_kmer_thres= 0.001
nextflow_config - Config default value correct: params.wfmash_sparse_map= 1.0
nextflow_config - Config default value correct: params.wfmash_chunks= 1
nextflow_config - Config default value correct: params.wfmash_hg_filter_ani_diff= 30
nextflow_config - Config default value correct: params.seqwish_min_match_length= 23
nextflow_config - Config default value correct: params.seqwish_transclose_batch= 10000000
nextflow_config - Config default value correct: params.seqwish_sparse_factor= 0.0
nextflow_config - Config default value correct: params.smoothxg_max_path_jump= 0
nextflow_config - Config default value correct: params.smoothxg_max_edge_jump= 0
nextflow_config - Config default value correct: params.smoothxg_poa_length= 700,900,1100
nextflow_config - Config default value correct: params.smoothxg_block_ratio_min= 0
nextflow_config - Config default value correct: params.smoothxg_pad_max_depth= 100
nextflow_config - Config default value correct: params.smoothxg_poa_padding= 0.001
nextflow_config - Config default value correct: params.smoothxg_poa_params= 1,19,39,3,81,1
nextflow_config - Config default value correct: params.smoothxg_consensus_prefix= Consensus_
nextflow_config - Config default value correct: params.smoothxg_poa_cpus= 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.schema_ignore_params= igenomes_base
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/PULL_REQUEST_TEMPLATE.md 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_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
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/plain'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 - WFMASH_MAP_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_MAP found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_MAP_COMMUNITY found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_APPROX_MAPPINGS_IN_CHUNKS found in conf/modules.config and Nextflow scripts.
modules_config - WFMASH_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SEQWISH found in conf/modules.config and Nextflow scripts.
modules_config - SMOOTHXG found in conf/modules.config and Nextflow scripts.
modules_config - GFAFFIX found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_UNCHOP found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_SORT found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_STATS found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_COLOR found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_POS found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_INV found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_UNCALLED found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_VIZ_COMPR found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_LAYOUT found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_DRAW_MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_DRAW_HEIGHT found in conf/modules.config and Nextflow scripts.
modules_config - VG_DECONSTRUCT found in conf/modules.config and Nextflow scripts.
modules_config - PAF2NET found in conf/modules.config and Nextflow scripts.
modules_config - NET2COMMUNITIES found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_COMMUNITIES found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_COMMUNITY found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ODGI_SQUEEZE 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: 3.2.0
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.2.0
Run at 2025-02-03 09:44:03

subwaystation · 2025-01-30T20:07:35Z

The linter seems wrong here?! In

pangenome/nextflow.config

Line 106 in d292756

includeConfig 'conf/base.config'

the line is uncommented. Or where else does the linter look? The link to the specification is broken and gives a 404.
@mashehu Maybe you have an idea?

heuermh · 2025-01-31T02:07:46Z

Got help on Slack, fix is in #239

heuermh · 2025-01-31T02:08:16Z

I don't understand this failure though
https://github.com/nf-core/pangenome/actions/runs/13057631753/job/36433443182?pr=237

Fix 1.1.3 release lint error(s)

subwaystation · 2025-01-31T07:21:04Z

I don't understand this failure though https://github.com/nf-core/pangenome/actions/runs/13057631753/job/36433443182?pr=237

Me neither.....

charles-plessy

Looks good to me.

docs/output.md

heuermh · 2025-02-04T22:11:49Z

Oh, I think I understand the issue now. Our release pull request has changes to download_pipeline.yml in it e.g.

- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+ uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0

But the failing CI build is still using the older version.

So do we just merge the release pull request and ignore this one CI failure?

subwaystation · 2025-02-05T10:14:49Z

Could be a hen and an egg problem.

subwaystation

This looks good to me. I also got the approval from @jfy133 that we can ignore the failing test and go forward with this.

subwaystation · 2025-02-08T19:55:52Z

Why is the AWS test skipped? We need this one to run through. There might still be a bug in fusion and we have to run it manually. If it does not run, I can't tell.

jfy133 · 2025-02-08T20:09:25Z

@subwaystation I think because it only happens on initial opening of the PR. Trigger a manual test via the action tab and we can check that instead

subwaystation · 2025-02-08T20:13:44Z

I did trigger it, but it is always skipped. What can I do? @jfy133

jfy133 · 2025-02-09T05:07:49Z

Looks like you did trigger it!

subwaystation · 2025-02-09T09:56:55Z

Alright, thanks to @jfy133 we can be happy https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4pN1X5F3w9wtaa and merge this @heuermh !

jfy133 · 2025-02-09T10:38:39Z

Let me know if you don't have force merge rights

subwaystation · 2025-02-09T10:48:55Z

I do have ;)

heuermh · 2025-02-09T15:55:46Z

🥳 Thank you, @subwaystation @jfy133 @charles-plessy!

subwaystation and others added 30 commits March 25, 2024 16:12

bump to 1.2.0dev

2ffef33

Merge pull request #195 from subwaystation/dev

6719020

bump to 1.2.0dev

update workflow svg

1708db9

finished makeup2

411a5dc

Merge pull request #199 from nf-core/workflow_svg

1aed918

update workflow svg

Template update for nf-core/tools version 2.14.0

cdc1494

Template update for nf-core/tools version 2.14.1

1e52981

Template update for nf-core/tools version 3.0.0

d4a3def

Template update for nf-core/tools version 3.0.1

f21fb92

Template update for nf-core/tools version 3.0.2

e7671c6

Template update for nf-core/tools version 3.1.0

62f8366

Template update for nf-core/tools version 3.1.1

782e1c6

Merged changes from nf-core template

67b3acf

Fix up invalid input values

a6622ad

Fix up incorrectly typed input values

407820f

Add exceptions to files_exist lint check

3c96fea

Removing unnecessary fastqc test files

62bf0eb

Remove samplesheet output channel from PIPELINE_INITIALIZATION

3ffab69

Update to nf-core/setup-nextflow@2 in custom CI jobs

6d2b02f

Add missing ch_versions channel

57aee62

Fix up pangenome workflow

973bbe9

Attempt to fix lint errors

a67f17e

Set validation lenientMode to true

f038844

Address review comments

0947d1f

Merge pull request #213 from heuermh/merging-template-updates

5a5941c

Merging template updates for versions 2.14.0 through 3.1.1

Update nf-core/smoothxg module to version 0.8.0

784a9af

Merge pull request #216 from heuermh/smoothxg-0.8.0

10beeb4

Update nf-core/smoothxg module to version 0.8.0

make n_haplotypes null

1d128e7

Merge pull request #220 from nf-core/i218

b1bca81

make parameter `n_haplotypes` null

Refactor authors to list of contributors

8fd5000

subwaystation and others added 5 commits January 30, 2025 12:30

prepare 1.1.3 release

38c1d9a

commit hidden file

5558242

prettier

6e611e8

Merge pull request #236 from subwaystation/dev

7c435e5

prepare new release 1.1.3 - marsupial

Resolve merge conflicts

63b639b

Merge pull request #238 from heuermh/dev

d292756

Resolve merge conflicts

heuermh added 2 commits January 30, 2025 16:31

Fix release lint error

ae0ff02

Retrigger CI checks

40c25e8

Merge pull request #239 from heuermh/1.1.3-release-lint

1fcf24e

Fix 1.1.3 release lint error(s)

charles-plessy approved these changes Feb 3, 2025

View reviewed changes

docs/output.md Outdated Show resolved Hide resolved

fix pipeline information header in output.md

f2b63fe

subwaystation approved these changes Feb 8, 2025

View reviewed changes

subwaystation merged commit 3d02bd1 into master Feb 9, 2025
41 of 42 checks passed

heuermh mentioned this pull request Feb 9, 2025

Apply changes from dev for download_pipeline.yml #240

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Release version 1.1.3 #237

Release version 1.1.3 #237

heuermh commented Jan 30, 2025

heuermh commented Jan 30, 2025

github-actions bot commented Jan 30, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Jan 30, 2025

heuermh commented Jan 31, 2025

heuermh commented Jan 31, 2025

subwaystation commented Jan 31, 2025

charles-plessy left a comment

heuermh commented Feb 4, 2025

subwaystation commented Feb 5, 2025

subwaystation left a comment

subwaystation commented Feb 8, 2025

jfy133 commented Feb 8, 2025

subwaystation commented Feb 8, 2025

jfy133 commented Feb 9, 2025

subwaystation commented Feb 9, 2025

jfy133 commented Feb 9, 2025

subwaystation commented Feb 9, 2025

heuermh commented Feb 9, 2025

Release version 1.1.3 #237

Release version 1.1.3 #237

Conversation

heuermh commented Jan 30, 2025

PR checklist

heuermh commented Jan 30, 2025

github-actions bot commented Jan 30, 2025 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

subwaystation commented Jan 30, 2025

heuermh commented Jan 31, 2025

heuermh commented Jan 31, 2025

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heuermh commented Feb 4, 2025

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subwaystation commented Feb 8, 2025

jfy133 commented Feb 8, 2025

subwaystation commented Feb 8, 2025

jfy133 commented Feb 9, 2025

subwaystation commented Feb 9, 2025

jfy133 commented Feb 9, 2025

subwaystation commented Feb 9, 2025

heuermh commented Feb 9, 2025

github-actions bot commented Jan 30, 2025 •

edited

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