Bring together the genomic and organellar workflows

[DLBPointon]

Attempt 1 to bring together the genomic and organellar subworkflows.

[sanger-tolsoft]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8bd6a54

+| ✅ 212 tests passed       |+
#| ❔  38 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• nextflow_config - Config manifest.version should end in dev: 0.6.0
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• 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!
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-ascc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-ascc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-ascc_logo_dark.png
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: lib/nfcore_external_java_deps.jar
• files_exist - File is ignored: lib/NfcoreSchema.groovy
• files_exist - File is ignored: lib/NfcoreTemplate.groovy
• files_exist - File is ignored: lib/Utils.groovy
• files_exist - File is ignored: lib/WorkflowMain.groovy
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: params.validationSchemaIgnoreParams
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.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/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-ascc_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml
• actions_awsfulltest - actions_awsfulltest
• template_strings - template_strings
• multiqc_config - multiqc_config

❔ 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: 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-ascc_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/Workflow.groovy
• files_exist - File not found check: lib/WorkflowAscc.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: .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 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 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.reads_type= hifi
• nextflow_config - Config default value correct: params.reads_layout= SINGLE
• nextflow_config - Config default value correct: params.kmer_length= 7.0
• nextflow_config - Config default value correct: params.seqkit_sliding= 100000
• nextflow_config - Config default value correct: params.seqkit_window= 6000
• nextflow_config - Config default value correct: params.n_neighbours= 13
• nextflow_config - Config default value correct: params.filter_cutoff= 1900000000
• nextflow_config - Config default value correct: params.coverage_reads_per_chunk= 1000000
• nextflow_config - Config default value correct: params.run_essentials= both
• nextflow_config - Config default value correct: params.run_kmers= genomic
• nextflow_config - Config default value correct: params.run_tiara= both
• nextflow_config - Config default value correct: params.run_coverage= both
• nextflow_config - Config default value correct: params.run_nt_blast= both
• nextflow_config - Config default value correct: params.run_html_report= off
• nextflow_config - Config default value correct: params.run_nr_diamond= both
• nextflow_config - Config default value correct: params.run_uniprot_diamond= both
• nextflow_config - Config default value correct: params.run_kraken= both
• nextflow_config - Config default value correct: params.run_fcsgx= both
• nextflow_config - Config default value correct: params.run_fcs_adaptor= both
• nextflow_config - Config default value correct: params.run_vecscreen= both
• nextflow_config - Config default value correct: params.run_btk_busco= genomic
• nextflow_config - Config default value correct: params.run_pacbio_barcodes= both
• nextflow_config - Config default value correct: params.run_organellar_blast= genomic
• nextflow_config - Config default value correct: params.run_autofilter_assembly= both
• nextflow_config - Config default value correct: params.run_create_btk_dataset= both
• nextflow_config - Config default value correct: params.run_merge_datasets= genomic
• nextflow_config - Config default value correct: params.run_decontaminate_fasta= both
• nextflow_config - Config default value correct: params.btk_busco_run_mode= conditional
• 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.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/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 - .github/.dockstore.yml 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: 25.10.0, Config: 25.10.0
• 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
• 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: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: workflowhub_update.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: linting.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: linting_comment.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• 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.
• base_config - SANGER_TOL_BTK found in conf/base.config and Nextflow scripts.
• base_config - BLAST_BLASTN found in conf/base.config and Nextflow scripts.
• base_config - COVERM_CONTIG found in conf/base.config and Nextflow scripts.
• base_config - FCSGX_RUNGX found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_MERGE found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_SORT found in conf/base.config and Nextflow scripts.
• base_config - VALIDATE_TAXID found in conf/base.config and Nextflow scripts.
• base_config - GET_KMER_COUNTS found in conf/base.config and Nextflow scripts.
• base_config - KRAKEN2_KRAKEN2 found in conf/base.config and Nextflow scripts.
• base_config - TIARA_TIARA found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - SANGER_TOL_BTK found in conf/modules.config and Nextflow scripts.
• modules_config - ORGANELLE_CONTAMINATION_RECOMMENDATIONS found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - MITO_ORGANELLAR_BLAST found in conf/modules.config and Nextflow scripts.
• modules_config - PLASTID_ORGANELLAR_BLAST found in conf/modules.config and Nextflow scripts.
• modules_config - TRAILINGNS found in conf/modules.config and Nextflow scripts.
• modules_config - TIARA_TIARA found in conf/modules.config and Nextflow scripts.
• modules_config - PARSE_FCSGX_RESULT found in conf/modules.config and Nextflow scripts.
• modules_config - FCSGX_RUNGX found in conf/modules.config and Nextflow scripts.
• modules_config - COVERM_CONTIG found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_EUK found in conf/modules.config and Nextflow scripts.
• modules_config - KMER_COUNT_DIM_REDUCTION_COMBINE_CSV found in conf/modules.config and Nextflow scripts.
• modules_config - AUTOFILTER_AND_CHECK_ASSEMBLY found in conf/modules.config and Nextflow scripts.
• modules_config - EXTRACT_CONTAMINANTS found in conf/modules.config and Nextflow scripts.
• modules_config - ASCC_MERGE_TABLES found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_BTK_DATASETS found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_BTK_DATASET found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - GENERATE_HTML_REPORT found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SLIDING found in conf/modules.config and Nextflow scripts.
• modules_config - BLAST_MAKEBLASTDB found in conf/modules.config and Nextflow scripts.
• modules_config - BLAST_BLASTN found in conf/modules.config and Nextflow scripts.
• modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - GET_LINEAGE_FOR_KRAKEN found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_PROK found in conf/modules.config and Nextflow scripts.
• modules_config - FCS_FCSADAPTOR_EUK found in conf/modules.config and Nextflow scripts.
• modules_config - SED_SED found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_ILLUMINA found in conf/modules.config and Nextflow scripts.
• modules_config - NCBITOOLS_VECSCREEN found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_VECSCREEN_RESULTS 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: 3.5.2
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 3.5.2
• Run at 2026-08-13 14:08:10

[DLBPointon]

This should run next to ASCC-prefect to ensure correctness