Replace tabix module by georgiakes · Pull Request #329 · nf-core/variantbenchmarking

georgiakes · 2026-10-02T09:25:02Z

Closes #323

PR checklist

github-actions · 2026-10-02T09:27:23Z

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

Posted for pipeline commit 6b2df94

+| ✅ 302 tests passed       |+
#| ❔   3 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_unchanged - File ignored due to lint config: docs/images/nf-core-variantbenchmarking_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-variantbenchmarking_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

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

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/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/pr-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-variantbenchmarking_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-variantbenchmarking_logo_light.png
files_exist - File found: docs/images/nf-core-variantbenchmarking_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: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.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-variantbenchmarking_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/WorkflowVariantbenchmarking.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: 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 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: 1.6.0dev
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.happy_comparison_engine= default
nextflow_config - Config default value correct: params.high_conf= true
nextflow_config - Config default value correct: params.min_sv_size= 0
nextflow_config - Config default value correct: params.max_sv_size= -1
nextflow_config - Config default value correct: params.min_allele_freq= -1.0
nextflow_config - Config default value correct: params.min_num_reads= -1
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking
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/
nf_test_content - 'tests/somatic_snv.nf.test' contains outdir parameter
nf_test_content - 'tests/somatic_snv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/somatic_snv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/somatic_snv.nf.test' contains outdir parameter
nf_test_content - 'tests/somatic_snv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/somatic_snv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/somatic_sv.nf.test' contains outdir parameter
nf_test_content - 'tests/somatic_sv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/somatic_sv.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/germline_small.nf.test' contains outdir parameter
nf_test_content - 'tests/germline_small.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/germline_small.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/germline_small.nf.test' contains outdir parameter
nf_test_content - 'tests/germline_small.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/germline_small.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/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/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/pr-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 - assets/nf-core-variantbenchmarking_logo_light.png matches the template
files_unchanged - docs/README.md 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.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings 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_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.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: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: 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 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 - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - HTSLIB_BGZIPTABIX found in conf/modules.config and Nextflow scripts.
modules_config - TABIX_BGZIPTABIX found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_SUBSAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - ADD_GT_STRELKA found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_FILTERMISSING found in conf/modules.config and Nextflow scripts.
modules_config - INJECT_MISSING_GT found in conf/modules.config and Nextflow scripts.
modules_config - VARIANTEXTRACTOR found in conf/modules.config and Nextflow scripts.
modules_config - SVYNC found in conf/modules.config and Nextflow scripts.
modules_config - RTGTOOLS_SVDECOMPOSE found in conf/modules.config and Nextflow scripts.
modules_config - SVTK_STANDARDIZE found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_LIFTOVERVCF found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - UCSC_LIFTOVER found in conf/modules.config and Nextflow scripts.
modules_config - GNU_SORT found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - REFORMAT_HEADER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_REHEADER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_RENAME_CHRS found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_CONTIGS found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_SPLIT_MULTI found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SURVIVOR_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_SNV found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_INDEL found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_ENSEMBLE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_MAJORITY found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_UNIFY_HEADER found in conf/modules.config and Nextflow scripts.
modules_config - REFORMAT_TRUTH found in conf/modules.config and Nextflow scripts.
modules_config - SURVIVOR_ENSEMBLE found in conf/modules.config and Nextflow scripts.
modules_config - REFORMAT_TRUTH_SV found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_SORT_SV found in conf/modules.config and Nextflow scripts.
modules_config - SURVIVOR_STATS found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - RTGTOOLS_FORMAT found in conf/modules.config and Nextflow scripts.
modules_config - RTGTOOLS_VCFEVAL found in conf/modules.config and Nextflow scripts.
modules_config - RTGTOOLS_BNDEVAL found in conf/modules.config and Nextflow scripts.
modules_config - RTGTOOLS_CNVEVAL found in conf/modules.config and Nextflow scripts.
modules_config - HAPPY_HAPPY found in conf/modules.config and Nextflow scripts.
modules_config - HAPPY_SOMPY found in conf/modules.config and Nextflow scripts.
modules_config - AARDVARK_COMPARE found in conf/modules.config and Nextflow scripts.
modules_config - SOMPY_FEATURES_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - TRUVARI_BENCH found in conf/modules.config and Nextflow scripts.
modules_config - SVANALYZER_SVBENCHMARK found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_CONCORDANCE found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_TP_BASE found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_TP_COMP found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_FN found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_FP found in conf/modules.config and Nextflow scripts.
modules_config - SUBTRACT_VCF_QUERY found in conf/modules.config and Nextflow scripts.
modules_config - SUBTRACT_VCF_TRUTH found in conf/modules.config and Nextflow scripts.
modules_config - WITTYER found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_INTERSECT_BENCH found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_TRUTH found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_VIEW_QUERY found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_FILTER_TRUTH_TP found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_FILTER_TRUTH_FN found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_FILTER_QUERY_TP found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_FILTER_QUERY_FP found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_REPORTS found in conf/modules.config and Nextflow scripts.
modules_config - PLOTS_METRICS found in conf/modules.config and Nextflow scripts.
modules_config - PLOTS_UPSET found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_DATAVZRD_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - DATAVZRD found in conf/modules.config and Nextflow scripts.
modules_config - HAPPY_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - PLOTS_SVLEN_DIST found in conf/modules.config and Nextflow scripts.
modules_config - SURVIVOR_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - VCF_TO_CSV found in conf/modules.config and Nextflow scripts.
modules_config - SOMPY_FEATURES_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SVTK_VCF2BED found in conf/modules.config and Nextflow scripts.
modules_config - BEDOPS_CONVERT2BED 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: 4.1.0
rocrate_readme_sync - RO-Crate description matches the README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.1.0
Run at 2026-10-02 14:07:14

github-actions · 2026-10-02T09:34:35Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ docker | latest-everything | Shard 1/7

See the full run for details.

kubranarci

I will keep checking PR, but in future can you please do not realign the code :D it creates so many changes to track and make the job hard.

kubranarci · 2026-10-02T10:56:43Z

+        // meta is shared by all test vcfs of a tool and tag, add the file name so each vcf joins with its own index
        TABIX_BGZIPTABIX(
-            REFORMAT_HEADER.out.output
+            REFORMAT_HEADER.out.output.map { meta, vcf -> [meta + [vcf_name: vcf.name], vcf, [], []] },


why vcf_name is required here?

I thought is was failing because the meta id would be the same for multiple samples.
I removed it and added groupBy since groupTuple is a legacy operator.

Hmm it doesn't run with version 25.10.4 though.

meta.id wont be the same as it is always unique (schema controls it)

This reverts commit 9297921.

georgiakes · 2026-10-02T13:52:05Z

I will keep checking PR, but in future can you please do not realign the code :D it creates so many changes to track and make the job hard.

Ohhh. Yeah really sorry for that. It will not happen again.

georgiakes added 2 commits October 2, 2026 11:11

Add htslib module

5171dd2

Replace tabix with htslib

fb89730

georgiakes added 2 commits October 2, 2026 11:43

Update snapshot

441cbf8

Update snapshot

f488ee1

georgiakes requested a review from kubranarci October 2, 2026 10:32

kubranarci reviewed Oct 2, 2026

View reviewed changes

georgiakes added 3 commits October 2, 2026 14:08

Publish tabix_bgziptabix output.

1c6d500

Use groupBy operator

9297921

Revert "Use groupBy operator"

8b84f99

This reverts commit 9297921.

georgiakes added 2 commits October 2, 2026 15:53

Remove vcf_name from meta

bde31d0

Remove failOnDupplicate

6b2df94

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Replace tabix module - #329

Replace tabix module#329
georgiakes wants to merge 9 commits into
nf-core:devfrom
georgiakes:replace-tabix-module

georgiakes commented Oct 2, 2026 •

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PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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❌ nf-test failed with latest Nextflow version

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georgiakes Oct 2, 2026

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georgiakes Oct 2, 2026

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kubranarci Oct 2, 2026

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georgiakes commented Oct 2, 2026

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georgiakes commented Oct 2, 2026 •

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github-actions Bot commented Oct 2, 2026 •

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

github-actions Bot commented Oct 2, 2026 •

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