Strip original contig splitting approach and preanno orf attempt3

[jfy133]

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
• If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
• 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 master 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 @jfy133,

It looks like this pull-request is has been made against the nf-core/funcscan master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/funcscan 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 lint overall result: Passed ✅

Posted for pipeline commit 5e19b8b

+| ✅ 312 tests passed       |+

✅ 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: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/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: assets/nf-core-funcscan_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-funcscan_logo_light.png
• files_exist - File found: docs/images/nf-core-funcscan_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: 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: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• 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-funcscan_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/WorkflowFuncscan.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 - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: params.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• 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 manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.2.0dev
• 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.taxa_classification_tool= mmseqs2
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_databases_id= Kalamari
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_searchtype= 2
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcaranks= kingdom,phylum,class,order,family,genus,species
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_taxlineage= 1
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_sensitivity= 5.0
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_orffilters= 2.0
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcamode= 3
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_votemode= 1
• nextflow_config - Config default value correct: params.annotation_tool= pyrodigal
• nextflow_config - Config default value correct: params.annotation_bakta_db_downloadtype= full
• nextflow_config - Config default value correct: params.annotation_bakta_mincontiglen= 1
• nextflow_config - Config default value correct: params.annotation_bakta_translationtable= 11
• nextflow_config - Config default value correct: params.annotation_bakta_gram= ?
• nextflow_config - Config default value correct: params.annotation_prokka_kingdom= Bacteria
• nextflow_config - Config default value correct: params.annotation_prokka_gcode= 11
• nextflow_config - Config default value correct: params.annotation_prokka_mincontiglen= 1
• nextflow_config - Config default value correct: params.annotation_prokka_evalue= 1e-06
• nextflow_config - Config default value correct: params.annotation_prokka_coverage= 80
• nextflow_config - Config default value correct: params.annotation_prokka_compliant= true
• nextflow_config - Config default value correct: params.annotation_prodigal_transtable= 11
• nextflow_config - Config default value correct: params.annotation_pyrodigal_transtable= 11
• nextflow_config - Config default value correct: params.amp_ampir_model= precursor
• nextflow_config - Config default value correct: params.amp_ampir_minlength= 10
• nextflow_config - Config default value correct: params.amp_ampcombi_cutoff= 0.0
• nextflow_config - Config default value correct: params.arg_amrfinderplus_identmin= -1.0
• nextflow_config - Config default value correct: params.arg_amrfinderplus_coveragemin= 0.5
• nextflow_config - Config default value correct: params.arg_amrfinderplus_translationtable= 11
• nextflow_config - Config default value correct: params.arg_deeparg_data_version= 2
• nextflow_config - Config default value correct: params.arg_deeparg_model= LS
• nextflow_config - Config default value correct: params.arg_deeparg_minprob= 0.8
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentevalue= 1e-10
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentidentity= 50
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentoverlap= 0.8
• nextflow_config - Config default value correct: params.arg_deeparg_numalignmentsperentry= 1000
• nextflow_config - Config default value correct: params.arg_fargene_hmmmodel= class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
• nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
• nextflow_config - Config default value correct: params.arg_fargene_translationformat= pearson
• nextflow_config - Config default value correct: params.arg_rgi_savejson= false
• nextflow_config - Config default value correct: params.arg_rgi_savetmpfiles= false
• nextflow_config - Config default value correct: params.arg_rgi_alignmenttool= BLAST
• nextflow_config - Config default value correct: params.arg_rgi_includeloose= false
• nextflow_config - Config default value correct: params.arg_rgi_includenudge= false
• nextflow_config - Config default value correct: params.arg_rgi_lowquality= false
• nextflow_config - Config default value correct: params.arg_rgi_data= NA
• nextflow_config - Config default value correct: params.arg_rgi_split_prodigal_jobs= true
• nextflow_config - Config default value correct: params.arg_abricate_db= ncbi
• nextflow_config - Config default value correct: params.arg_abricate_minid= 80
• nextflow_config - Config default value correct: params.arg_abricate_mincov= 80
• nextflow_config - Config default value correct: params.bgc_antismash_contigminlength= 1000
• nextflow_config - Config default value correct: params.bgc_antismash_hmmdetectionstrictness= relaxed
• nextflow_config - Config default value correct: params.bgc_antismash_taxon= bacteria
• nextflow_config - Config default value correct: params.bgc_deepbgc_score= 0.5
• nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxproteingap= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxnuclgap= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_minnucl= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_minproteins= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_mindomains= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_minbiodomains= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_classifierscore= 0.5
• nextflow_config - Config default value correct: params.bgc_gecco_cds= 3
• nextflow_config - Config default value correct: params.bgc_gecco_pfilter= 1e-09
• nextflow_config - Config default value correct: params.bgc_gecco_threshold= 0.8
• nextflow_config - Config default value correct: params.bgc_gecco_edgedistance= 0
• nextflow_config - Config default value correct: params.arg_hamronization_summarizeformat= tsv
• 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= 128.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.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/
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/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/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-funcscan_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-funcscan_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (313 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: branch.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awstest.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
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - GUNZIP found in conf/base.config and Nextflow scripts.
• base_config - UNTAR found in conf/base.config and Nextflow scripts.
• base_config - PROKKA found in conf/base.config and Nextflow scripts.
• base_config - PRODIGAL_GBK found in conf/base.config and Nextflow scripts.
• base_config - BAKTA_BAKTA found in conf/base.config and Nextflow scripts.
• base_config - ABRICATE_RUN found in conf/base.config and Nextflow scripts.
• base_config - AMRFINDERPLUS_RUN found in conf/base.config and Nextflow scripts.
• base_config - DEEPARG_DOWNLOADDATA found in conf/base.config and Nextflow scripts.
• base_config - DEEPARG_PREDICT found in conf/base.config and Nextflow scripts.
• base_config - FARGENE found in conf/base.config and Nextflow scripts.
• base_config - RGI_MAIN found in conf/base.config and Nextflow scripts.
• base_config - AMPIR found in conf/base.config and Nextflow scripts.
• base_config - AMPLIFY_PREDICT found in conf/base.config and Nextflow scripts.
• base_config - AMP_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
• base_config - MACREL_CONTIGS found in conf/base.config and Nextflow scripts.
• base_config - BGC_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
• base_config - ANTISMASH_ANTISMASHLITE found in conf/base.config and Nextflow scripts.
• base_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/base.config and Nextflow scripts.
• base_config - DEEPBGC_DOWNLOAD found in conf/base.config and Nextflow scripts.
• base_config - DEEPBGC_PIPELINE found in conf/base.config and Nextflow scripts.
• base_config - GECCO_RUN found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_ABRICATE found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_DEEPARG found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_RGI found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_FARGENE found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_SUMMARIZE found in conf/base.config and Nextflow scripts.
• base_config - AMPCOMBI found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_DATABASES found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_CREATEDB found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_CREATETSV found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
• modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
• modules_config - PYRODIGAL found in conf/modules.config and Nextflow scripts.
• modules_config - ABRICATE_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - AMRFINDERPLUS_UPDATE found in conf/modules.config and Nextflow scripts.
• modules_config - AMRFINDERPLUS_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPARG_DOWNLOADDATA found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPARG_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - FARGENE found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_CARD found in conf/modules.config and Nextflow scripts.
• modules_config - RGI_CARDANNOTATION found in conf/modules.config and Nextflow scripts.
• modules_config - RGI_MAIN found in conf/modules.config and Nextflow scripts.
• modules_config - AMPIR found in conf/modules.config and Nextflow scripts.
• modules_config - AMPLIFY_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - AMP_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - MACREL_CONTIGS found in conf/modules.config and Nextflow scripts.
• modules_config - BGC_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - ANTISMASH_ANTISMASHLITE found in conf/modules.config and Nextflow scripts.
• modules_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPBGC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPBGC_PIPELINE found in conf/modules.config and Nextflow scripts.
• modules_config - GECCO_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_ABRICATE found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_DEEPARG found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_RGI found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_FARGENE found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_SUMMARIZE found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_HAMRONIZATION found in conf/modules.config and Nextflow scripts.
• modules_config - ARG_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - AMPCOMBI found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_AMPCOMBI found in conf/modules.config and Nextflow scripts.
• modules_config - AMP_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - COMBGC found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_COMBGC found in conf/modules.config and Nextflow scripts.
• modules_config - BGC_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - DRAMP_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: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-05-30 06:42:56

[jasmezz]

Some docs comments

[Darcy220606]

looks fine to me 👍🏽 Just this bit about the preannotated files as input in this PR...