Move to 2.2.0

[Thibault-Poinsignon]

Version 2.2.0

Added

• Subworkflows meta.yml
• Module FAIDX for chromosomes sizes calculation
• TRIMGALORE module for 5' clipping (see Improve pipeline for Arima Hi-C protocol #225)
• CALDER2 compartments calling (see '--compartments_caller' option)
• Local FILTER_CHROMSIZE module (in order to apply CALDER2 without error)
• Optional '--min_size' parameter for chromosome selection
• Default MIN_FRAG_SIZE, MAX_FRAG_SIZE, MIN_INSERT_SIZE and MAX_INSERT_SIZE values for Arima and ArimV2 protocols

Removed

• Module GETCHROMSIZES (replaced by FAIDX)
• Version channels from subworkflows (tools versions gathering still a WIP)

Fixed

• MATPLOTLIB warning derails parsing cooltools version in collated_versions.yml during NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS #227: MPLCONFIGDIR is set to "${baseDir}/mplconfig"
• reported bugs #62: a single number can be given as BIN_SIZES without error
• Improve pipeline for Arima Hi-C protocol #225:TRIMGALORE remove the first 5 bases of the 5' end and
  fragments and inserts size min/max settings are set to recommended values if Arima/ArimaV2 is used
• Bug from COOLER_CLOAD deprecated "pairs" ext.args calling
• Bug on the cooler "add resolution" step caused by module COOLER_CLOAD update

Updated

• All nf-core modules (including topics channel)
• Modules path
• "channel" syntax with lowercase c
• Components names in subworkflows meta.yml
• COOLER_CLOAD inputs and outputs
• BWA_MEM inputs
• SAMTOOL_SORT inputs
• UTILS_NFSCHEMA_PLUGIN inputs and outputs
• Markdown settings
• Template files
• nf-core version to 3.5.0

PR checklist

• This comment contains a description of changes (with reason).
• 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,singularity --outdir <OUTDIR>).
• Usage Documentation in docs/usage.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 bb9d3a1

+| ✅ 259 tests passed       |+
#| ❔   1 tests were ignored |#

Details

❔ Tests ignored:

• schema_params - schema_params

✅ 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: 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/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: assets/nf-core-hic_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-hic_logo_light.png
• files_exist - File found: docs/images/nf-core-hic_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: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.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 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-hic_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/WorkflowHic.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.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: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• 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: 2.2.0dev
• 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.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.processing= hicpro
• nextflow_config - Config default value correct: params.fastq_chunks_size= 20000000
• nextflow_config - Config default value correct: params.min_mapq= 10
• nextflow_config - Config default value correct: params.bwt2_opts_end2end= --very-sensitive --end-to-end --reorder
• nextflow_config - Config default value correct: params.bwt2_opts_trimmed= --very-sensitive --end-to-end --reorder
• nextflow_config - Config default value correct: params.bwa_opts= -5SP -T0
• nextflow_config - Config default value correct: params.pairtools_parse_opts= --walks-policy 5unique
• nextflow_config - Config default value correct: params.bin_size= 1000000
• nextflow_config - Config default value correct: params.ice_filter_low_count_perc= 0.02
• nextflow_config - Config default value correct: params.ice_eps= 0.1
• nextflow_config - Config default value correct: params.ice_max_iter= 100
• nextflow_config - Config default value correct: params.balancing_opts= --force
• nextflow_config - Config default value correct: params.min_size= 0
• nextflow_config - Config default value correct: params.res_dist_decay= 250000
• nextflow_config - Config default value correct: params.tads_caller= insulation
• nextflow_config - Config default value correct: params.compartments_caller= cooltools
• nextflow_config - Config default value correct: params.res_tads= 40000
• nextflow_config - Config default value correct: params.res_compartments= 250000
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.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/
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - 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-hic_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-hic_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-hic_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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.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: 25.04.0, Config: 25.04.0
• 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
• 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'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.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: awstest.yml
• actions_schema_validation - Workflow validation passed: release-announcements.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'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - GET_RESTRICTION_FRAGMENTS found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - TRIM_READS found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN_TRIMMED found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_BOWTIE2 found in conf/modules.config and Nextflow scripts.
• modules_config - COMBINE_MATES found in conf/modules.config and Nextflow scripts.
• modules_config - GET_VALID_INTERACTION found in conf/modules.config and Nextflow scripts.
• modules_config - GET_VALID_INTERACTION_DNASE found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_VALID_INTERACTION found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - HICPRO2PAIRS found in conf/modules.config and Nextflow scripts.
• modules_config - BUILD_CONTACT_MAPS found in conf/modules.config and Nextflow scripts.
• modules_config - ICE_NORMALIZATION found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_PARSE found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_RESTRICT found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_SPLIT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_DEDUP found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_SELECT found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRTOOLS_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - PAIRIX found in conf/modules.config and Nextflow scripts.
• modules_config - HIC_PLOT_DIST_VS_COUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_MAKEBINS found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_CLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_BALANCE found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_DUMP found in conf/modules.config and Nextflow scripts.
• modules_config - SPLIT_COOLER_DUMP found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_ZOOMIFY found in conf/modules.config and Nextflow scripts.
• modules_config - COOLTOOLS_EIGSCIS found in conf/modules.config and Nextflow scripts.
• modules_config - COOLTOOLS_INSULATION found in conf/modules.config and Nextflow scripts.
• modules_config - HIC_FIND_TADS found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2026-03-10 10:55:00

[nservant]

This version looks good to me ! thank you @Thibault-Poinsignon
@maxulysse, any advice for the tests which are still failing ? Could we move forward like this.
We would like to release a new stable version asap.

[maxulysse]

This version looks good to me ! thank you @Thibault-Poinsignon @maxulysse, any advice for the tests which are still failing ? Could we move forward like this. We would like to release a new stable version asap.

I'd recommend to try and merge #233 and/or #234 to have a minimal test using nf-test

[Thibault-Poinsignon]

All the checks are now successful with the two template updates. I'm running some full tests again to verify that everything is still working properly.