[GH-219] Added assembly mode for HiC

[GallVp]

PR checklist

• Add hic_juicer_pre_assembly_mode flag #219
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41dd263

+| ✅ 179 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗  24 tests had warnings |!

❗ Test warnings:

• local_component_structure - ncbi_fcs_gx_krona_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - circos.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - kraken2_krona_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - splitbundlefile.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - linearsynteny.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - assemblathon_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - kraken2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dnadiff.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - colourbundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - createreport.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - getfastalength.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - hic2html.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - relabelfastalength.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - ncbi_fcs_gx_setup_sample.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - generatekaryotype.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - relabelbundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - ncbi_fcs_gx_screen_samples.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filtersortfasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - mummer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - fasta_synteny.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - fq2hic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - fasta_kraken2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - ncbi_fcs_gx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-assemblyqc_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: tests/default.nf.test
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: validation.help.beforeText
• nextflow_config - Config variable ignored: validation.help.afterText
• nextflow_config - Config variable ignored: validation.summary.beforeText
• nextflow_config - Config variable ignored: validation.summary.afterText
• nf_test_content - 'tests/nextflow.config' checking ignored
• 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 does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File does not exist: assets/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_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_nf_test - actions_nf_test
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
• template_strings - template_strings
• 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: .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: main.nf
• 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-assemblyqc_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/WorkflowAssemblyqc.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• 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 found: validation.help.command
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 3.0.0dev
• 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.check_sequence_duplicates= true
• nextflow_config - Config default value correct: params.assemblathon_stats_n_limit= 100
• nextflow_config - Config default value correct: params.gfastats_skip= true
• nextflow_config - Config default value correct: params.ncbi_fcs_adaptor_skip= true
• nextflow_config - Config default value correct: params.ncbi_fcs_gx_skip= true
• nextflow_config - Config default value correct: params.contamination_stops_pipeline= true
• nextflow_config - Config default value correct: params.tidk_skip= true
• nextflow_config - Config default value correct: params.tidk_filter_size_bp= 1000000
• nextflow_config - Config default value correct: params.busco_skip= true
• nextflow_config - Config default value correct: params.lai_skip= true
• nextflow_config - Config default value correct: params.kraken2_skip= true
• nextflow_config - Config default value correct: params.hic_skip_fastqc= true
• nextflow_config - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
• nextflow_config - Config default value correct: params.hic_alphanumeric_sort= true
• nextflow_config - Config default value correct: params.hic_mapq= 1
• nextflow_config - Config default value correct: params.merqury_skip= true
• nextflow_config - Config default value correct: params.merqury_kmer_length= 21
• nextflow_config - Config default value correct: params.synteny_skip= true
• nextflow_config - Config default value correct: params.synteny_mummer_skip= true
• nextflow_config - Config default value correct: params.synteny_plotsr_skip= true
• nextflow_config - Config default value correct: params.synteny_between_input_assemblies= true
• nextflow_config - Config default value correct: params.synteny_mummer_plot_type= both
• nextflow_config - Config default value correct: params.synteny_mummer_max_gap= 1000000
• nextflow_config - Config default value correct: params.synteny_mummer_min_bundle_size= 1000000
• nextflow_config - Config default value correct: params.synteny_color_by_contig= true
• nextflow_config - Config default value correct: params.synteny_plotsr_seq_label= Chr
• nextflow_config - Config default value correct: params.orthofinder_skip= true
• 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
• 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
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/linting_comment.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
• readme - README Nextflow minimum version badge matched config. Badge: 24.10.5, Config: 24.10.5
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• 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: linting.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: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - NCBI_FCS_GX_SCREEN_SAMPLES found in conf/base.config and Nextflow scripts.
• base_config - KRAKEN2 found in conf/base.config and Nextflow scripts.
• base_config - BWA_MEM found in conf/base.config and Nextflow scripts.
• base_config - SAMBLASTER found in conf/base.config and Nextflow scripts.
• base_config - JUICERTOOLS_PRE found in conf/base.config and Nextflow scripts.
• base_config - DNADIFF found in conf/base.config and Nextflow scripts.
• base_config - MERQURY_HAPMERS found in conf/base.config and Nextflow scripts.
• base_config - CREATEREPORT found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• 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: 3.3.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.3.1
• Run at 2025-06-18 07:08:25