Allow subtyping (ECTYPER) for all Escherichia species.

[kylacochrane]

This PR updates mikrokondo’s sample routing logic in the nextflow.config to send all Escherichia species to the ECTyper subtyping tool, instead of only samples explicitly labeled as Escherichia coli.

With the latest ECTyper updates (v2.0.0), virulence gene detection is now supported, making it valuable for broader Escherichia species beyond E. coli.

An E.albertii sample (fastq files) was run through mikrokondo to ensure it was run through ECTYPERv2.0.0 and the results were as expected.

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 60538dc

+| ✅ 228 tests passed       |+
#| ❔  35 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

• nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
• nextflow_config - Config manifest.version should end in dev: 0.8.1
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_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
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/usage.md
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: ro-crate-metadata.json
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: params.max_cpus
• files_unchanged - File does not exist: 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 does not exist: assets/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ 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: 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/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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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: modules.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-mikrokondo_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/WorkflowMikrokondo.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-validation 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 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.platform= illumina
• nextflow_config - Config default value correct: params.long_read_opt= nanopore
• 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.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 2000.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• 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.tracedir= null/pipeline_info
• nextflow_config - Config default value correct: params.stage_in_mode= symlink
• nextflow_config - Config default value correct: params.validationS3PathCheck= true
• nextflow_config - Config default value correct: params.skip_read_merging= true
• nextflow_config - Config default value correct: params.skip_bakta= true
• nextflow_config - Config default value correct: params.skip_ont_header_cleaning= true
• nextflow_config - Config default value correct: params.ec_opid= 90
• nextflow_config - Config default value correct: params.ec_opcov= 90
• nextflow_config - Config default value correct: params.ec_hpid= 95
• nextflow_config - Config default value correct: params.ec_hpcov= 50
• nextflow_config - Config default value correct: params.ec_enable_verification= true
• nextflow_config - Config default value correct: params.ec_pathpid= 90
• nextflow_config - Config default value correct: params.ec_pathcov= 50
• nextflow_config - Config default value correct: params.sr_full_cgmlst= true
• nextflow_config - Config default value correct: params.fp_average_quality= 25
• nextflow_config - Config default value correct: params.fp_cut_tail_mean_quality= 15
• nextflow_config - Config default value correct: params.fp_cut_tail_window_size= 4
• nextflow_config - Config default value correct: params.fp_complexity_threshold= 20
• nextflow_config - Config default value correct: params.fp_qualified_phred= 15
• nextflow_config - Config default value correct: params.fp_unqualified_percent_limit= 40
• nextflow_config - Config default value correct: params.fp_polyg_min_len= 10
• nextflow_config - Config default value correct: params.fp_polyx_min_len= 10
• nextflow_config - Config default value correct: params.fp_illumina_length_min= 35
• nextflow_config - Config default value correct: params.fp_illumina_length_max= 400
• nextflow_config - Config default value correct: params.fp_single_end_length_min= 1000
• nextflow_config - Config default value correct: params.lx_min_evalue= 0.0001
• nextflow_config - Config default value correct: params.lx_min_dna_len= 1
• nextflow_config - Config default value correct: params.lx_min_aa_len= 1
• nextflow_config - Config default value correct: params.lx_max_dna_len= 10000000
• nextflow_config - Config default value correct: params.lx_max_aa_len= 10000000
• nextflow_config - Config default value correct: params.lx_min_dna_ident= 80.0
• nextflow_config - Config default value correct: params.lx_min_aa_ident= 80.0
• nextflow_config - Config default value correct: params.lx_min_dna_match_cov= 80.0
• nextflow_config - Config default value correct: params.lx_min_aa_match_cov= 80.0
• nextflow_config - Config default value correct: params.lx_max_target_seqs= 10
• nextflow_config - Config default value correct: params.lx_extraction_mode= raw
• nextflow_config - Config default value correct: params.lx_report_mode= normal
• nextflow_config - Config default value correct: params.lx_report_prop= locus_name
• nextflow_config - Config default value correct: params.lx_report_max_ambig= 0
• nextflow_config - Config default value correct: params.lx_report_max_stop= 0
• nextflow_config - Config default value correct: params.target_depth= 100
• nextflow_config - Config default value correct: params.min_reads= 1000
• nextflow_config - Config default value correct: params.ba_min_contig_length= 200
• nextflow_config - Config default value correct: params.qt_min_contig_length= 1000
• nextflow_config - Config default value correct: params.mh_min_kmer= 10
• nextflow_config - Config default value correct: params.flye_read_type= hq
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• pipeline_todos - No TODO strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: spellcheck.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: doc.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'
• base_config - conf/base.config found and not ignored.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - PUBLISH_FINAL_READS found in conf/modules.config and Nextflow scripts.
• modules_config - PUBLISH_FINAL_ASSEMBLIES found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_EXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_SEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_REPORT found in conf/modules.config and Nextflow scripts.
• modules_config - REPORT found in conf/modules.config and Nextflow scripts.
• modules_config - IDENTIFY_POINTDB found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_SELECT found in conf/modules.config and Nextflow scripts.
• modules_config - LOCIDEX_SUMMARIZE found in conf/modules.config and Nextflow scripts.
• modules_config - REPORT_AGGREGATE found in conf/modules.config and Nextflow scripts.
• modules_config - BIN_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - COMBINE_DATA found in conf/modules.config and Nextflow scripts.
• modules_config - GZIP_FILES found in conf/modules.config and Nextflow scripts.
• modules_config - CHECK_ONT found in conf/modules.config and Nextflow scripts.
• modules_config - PARSE_MASH found in conf/modules.config and Nextflow scripts.
• modules_config - PARSE_KRAKEN found in conf/modules.config and Nextflow scripts.
• modules_config - READ_SCAN found in conf/modules.config and Nextflow scripts.
• modules_config - PARSE_FASTP found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
• modules_config - RASUSA found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_SIZE found in conf/modules.config and Nextflow scripts.
• modules_config - QUAST found in conf/modules.config and Nextflow scripts.
• modules_config - CHECKM_LINEAGEWF found in conf/modules.config and Nextflow scripts.
• modules_config - BANDAGE_IMAGE found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN found in conf/modules.config and Nextflow scripts.
• modules_config - MASH_ESTIMATE found in conf/modules.config and Nextflow scripts.
• modules_config - MLST found in conf/modules.config and Nextflow scripts.
• modules_config - STARAMR found in conf/modules.config and Nextflow scripts.
• modules_config - MOBSUITE_RECON found in conf/modules.config and Nextflow scripts.
• modules_config - MASH_SKETCH found in conf/modules.config and Nextflow scripts.
• modules_config - MASH_PASTE found in conf/modules.config and Nextflow scripts.
• modules_config - MASH_SCREEN found in conf/modules.config and Nextflow scripts.
• modules_config - REMOVE_CONTAMINANTS found in conf/modules.config and Nextflow scripts.
• modules_config - FLYE_ASSEMBLE found in conf/modules.config and Nextflow scripts.
• modules_config - SPADES_ASSEMBLE found in conf/modules.config and Nextflow scripts.
• modules_config - UNICYCLER_ASSEMBLE found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_MAP found in conf/modules.config and Nextflow scripts.
• modules_config - SAM_TO_BAM found in conf/modules.config and Nextflow scripts.
• modules_config - RACON_POLISH found in conf/modules.config and Nextflow scripts.
• modules_config - PILON_ITER found in conf/modules.config and Nextflow scripts.
• modules_config - MEDAKA_POLISH found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_DB_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_ANNOTATE found in conf/modules.config and Nextflow scripts.
• modules_config - ABRICATE found in conf/modules.config and Nextflow scripts.
• modules_config - ECTYPER found in conf/modules.config and Nextflow scripts.
• modules_config - KLEBORATE found in conf/modules.config and Nextflow scripts.
• modules_config - SPATYPER found in conf/modules.config and Nextflow scripts.
• modules_config - SISTR found in conf/modules.config and Nextflow scripts.
• modules_config - LISSERO found in conf/modules.config and Nextflow scripts.
• modules_config - SHIGEIFINDER found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - REPORT_PIPELINE_PARAMETERS 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: 3.1.1

Run details

• nf-core/tools version 3.1.1
• Run at 2025-08-11 15:14:16

[ChristyPeterson]

Formatting changes looked appropriate.