snap, version update

[robert-a-forsyth]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b5938f2

+| ✅ 178 tests passed       |+
#| ❔  21 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗ 144 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• 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 lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• 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 meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• local_component_structure - tumor_only_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - tumor_normal_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/lrsomatic/lrsomatic/.github/workflows/awstest.yml
• schema_params - schema_params

❔ 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: 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/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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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: 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-lrsomatic_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/WorkflowLrsomatic.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.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.1.0dev
• 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.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.save_secondary_alignment= true
• nextflow_config - Config default value correct: params.ascat_penalty= 150
• nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
• nextflow_config - Config default value correct: params.ascat_min_counts= 10
• nextflow_config - Config default value correct: params.ascat_min_map_qual= 10
• nextflow_config - Config default value correct: params.ascat_longread_bins= 2000
• nextflow_config - Config default value correct: params.ascat_allelecounter_flags= -f 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.normal_fiber= true
• 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 - LICENSE matches the template
• files_unchanged - .github/.dockstore.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/sendmail_template.txt 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
• readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• 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'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains '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 - ENSEMBLVEP_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.1
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2025-11-28 15:16:07

[Copilot]

Pull request overview

This PR transitions the pipeline from the stable v1.0.0 release to the v1.1.0dev development version. It updates version references across configuration files, test snapshots, and metadata, while also adding the Zenodo DOI citation information that was finalized for the v1.0.0 release.

Key changes:

• Version bumped from 1.0.0 to 1.1.0dev across all configuration files
• CHANGELOG updated to reflect v1.0.0 release date and prepare for v1.1.0
• Zenodo DOI updated from placeholder to actual DOI (10.5281/zenodo.17751829)

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/default.nf.test.snap	Updated version reference in test snapshots and refreshed timestamp
ro-crate-metadata.json	Updated workflow status to "InProgress", version to 1.1.0dev, URLs to dev branch, and refreshed UUIDs
nextflow.config	Bumped version from 1.0.0 to 1.1.0dev
assets/multiqc_config.yml	Changed report URL from v1.0.0 release tag to dev branch tree
README.md	Updated Zenodo DOI from placeholder to actual value and uncommented citation text
CHANGELOG.md	Added v1.0.0 release entry with date and created new v1.1.0 section
.nf-core.yml	Updated template version from 1.0.0 to 1.1.0dev

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[Copilot]

The version should be v1.1.0dev (with 'dev' suffix) to match the version specified in other files like nextflow.config, .nf-core.yml, and ro-crate-metadata.json, where the version is consistently set to 1.1.0dev.

Suggested change

	## v1.1.0 - [date]
	## v1.1.0dev - [date]

[Copilot]

The v1.1.0 section is empty with no description of changes. Since this is a development version being prepared, it should either:

1. Include a placeholder like Initial development for v1.1.0 or Development version - changes to be documented
2. List the actual changes being prepared for this version

Empty changelog sections make it difficult for users to understand what's changing between versions.

Suggested change

	Development version - changes to be documented