Fix naming collisions

[Kevin-Brockers]

PR checklist

close #440
close #467
close #510

Fixes the issues above - I hope this is sufficient.
The suggested solution for: Performing one IP vs multiple different controls is to encode those comparison as multiple samples in the sample sheet, however this would trigger many unnecessary preprocessing (fastq qcs and alignments) of the same IP samples. Ideally we would avoid that.

However, I am not sure how often those situations will occur.

• If you've fixed a bug or added code that should be tested, add tests!
• 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.
• 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 f83b1d6

+| ✅ 267 tests passed       |+
#| ❔   2 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

• nextflow_config - Config default ignored: params.bamtools_filter_pe_config
• nextflow_config - Config default ignored: params.bamtools_filter_se_config

❔ Tests fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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-chipseq_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-chipseq_logo_light.png
• files_exist - File found: docs/images/nf-core-chipseq_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-chipseq_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/WorkflowChipseq.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.fragment_size= 200
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.aligner= bwa
• nextflow_config - Config default value correct: params.broad_cutoff= 0.1
• nextflow_config - Config default value correct: params.min_reps_consensus= 1
• nextflow_config - Config default value correct: params.deseq2_vst= 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
• nextflow_config - Config default value correct: params.fingerprint_bins= 500000
• 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/chromap.nf.test' contains outdir parameter
• nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/chromap.nf.test' contains outdir parameter
• 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/bowtie2.nf.test' contains outdir parameter
• nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/bowtie2.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
• nf_test_content - 'tests/star.nf.test' contains outdir parameter
• nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/star.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
• 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-chipseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-chipseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-chipseq_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_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'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awstest.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 - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
• modules_config - KHMER_UNIQUEKMERS found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
• modules_config - GTF2BED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - GENOME_BLACKLIST_REGIONS found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - CHROMAP_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - CHROMAP_CHROMAP found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MERGESAMFILES found in conf/modules.config and Nextflow scripts.
• modules_config - BAMTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - BAM_REMOVE_ORPHANS found in conf/modules.config and Nextflow scripts.
• modules_config - PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_COLLECTMULTIPLEMETRICS found in conf/modules.config and Nextflow scripts.
• modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_COMPUTEMATRIX found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTPROFILE found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTHEATMAP found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTFINGERPRINT found in conf/modules.config and Nextflow scripts.
• modules_config - MACS3_CALLPEAK found in conf/modules.config and Nextflow scripts.
• modules_config - FRIP_SCORE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_CUSTOM_PEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - PLOT_MACS3_QC found in conf/modules.config and Nextflow scripts.
• modules_config - PLOT_HOMER_ANNOTATEPEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - MACS3_CONSENSUS found in conf/modules.config and Nextflow scripts.
• modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - ANNOTATE_BOOLEAN_PEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - DESEQ2_QC found in conf/modules.config and Nextflow scripts.
• modules_config - IGV found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC 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: 3.5.2
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 3.5.2
• Run at 2026-05-02 21:55:43