renamed metadata fields

[dfornika]

Renaming metadata field names as requested by @apetkau and @jrober84 (see Issue #148)

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 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.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @dfornika,

It looks like this pull-request is has been made against the phac-nml/mikrokondo main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/mikrokondo dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c0dd307

+| ✅ 228 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗  81 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• files_exist - File not found: ro-crate-metadata.json
• 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/
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• schema_lint - Schema 'description' should be 'Mikrokondo'
  Found: 'Mikrokondo beta'
• local_component_structure - locidex_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - spatyper.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mash_screen.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - kleborate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sam_to_bam.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - seqkit_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - combine_data.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - pilon_polisher.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - locidex_select.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sistr.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - seqtk_sample.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mash_sketch.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - chopper_trim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - seqtk_fasta_fastq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - remove_contaminants.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - lissero.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - kraken.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bakta_download_db.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - pilon_polish.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - select_pointfinder.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mash_estimate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mash_paste.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - quast_assembly.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - abricate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - download_gtdb.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - rasusa.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - fastp_trim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - checkm_lineagewf.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - parse_mash.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - locidex_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bakta_annotate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - shigatyper.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - minimap2_index.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - kat_hist.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - minimap2_map.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - read_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - parse_kat.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mob_recon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - gzip_files.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mlst.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - flye_assemble.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bandage_image.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - parse_kraken.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - fastqscan.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - check_ont.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bin_kraken2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - locidex_summarize.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - unicycler_assemble.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - parse_fastp.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - staramr.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - medaka_polish.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - ectyper.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - racon_polish.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - seqkit_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - spades_assemble.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - seqtk_size.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - report_aggregate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - locidex_search.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - shigeifinder.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - split_metagenomic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - annotate_genomes.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - hybrid_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - create_index.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - GTDB_Mash.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - locidex.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - determine_species.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - assemble_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - download_bakta_db.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - clean_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - polish_assemblies.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - subtype_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qc_assemblies.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• nfcore_yml - nf-core version in .nf-core.yml is not set to the latest version. Should be 3.2.0 but was 3.0.2

❔ 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
• 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.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 manifest.version does not contain dev for release: 0.5.0
• 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.override_allele_scheme=
• 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.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
• files_unchanged - .github/workflows/linting_comment.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 - 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: branch.yml
• actions_schema_validation - Workflow validation passed: doc.yml
• actions_schema_validation - Workflow validation passed: spellcheck.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• version_consistency - Version tags are numeric and consistent between container, release tag and config.
• included_configs - Pipeline config includes custom configs.

Run details

• nf-core/tools version 3.2.0
• Run at 2025-02-04 00:21:03

[dfornika]

In order to add a qc_status_read_length field, should we add a param to define the min_read_length (or min_mean_read_length)?

[apetkau]

Thanks so much @dfornika, this is awesome work 😄.

For your question on qc_status_read_length, that is a good point about adding a parameter for min_mean_read_length. @mattheww95 is this something that already exists in mikrokondo? As in a check to make sure the mean read length is over a threshold?

[apetkau]

Could you align this with the other text (I assume there's a tab here where there should be spaces).

[mattheww95]

Just following up on this PR. I reached out to @dfornika to mention that I can finish off this PR for him. I just had to wrap something else up.

I did have some questions related to the two new fields, the average read length one will not be too hard to add. But I want to verify some of the requirements for the new fields.