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Merge pull request #487 from Kevin-Brockers/dev_topic_channel_adaptation
Updating nf-core modules and subworkflows, including preparation for topics
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‎.nf-core.yml‎

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- config_defaults:
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- params.bamtools_filter_se_config
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- params.bamtools_filter_pe_config
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nf_core_version: 3.5.1
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nf_core_version: 3.5.2
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repository_type: pipeline
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template:
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author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v2.2.0dev - [date]
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## v2.2.0dev - 2026-03-14
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### Enhancements & fixes
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- [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.
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- [[PR #462](https://github.com/nf-core/chipseq/pull/462)] - Updated pipeline template to [nf-core/tools 3.2.1](https://github.com/nf-core/tools/releases/tag/3.2.1)
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- [[#468](https://github.com/nf-core/chipseq/issues/468)] - Changed bigWig generation to use `-bga` option instead of `-bg` in `bedtools genomecov` for lower background levels and better IGV visualization. Users can revert to previous behavior using configuration. See [documentation](https://nf-co.re/chipseq/dev/docs/output/#normalised-bigwig-files) for details.
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- [[#484](https://github.com/nf-core/chipseq/issues/484)] - Updated modules and subworkflows
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- [[#483](https://github.com/nf-core/chipseq/issues/483)] - Updated nf-core related things to topics, still a few nf-core modules are pending and the local modules
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need to be fixed.
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- [[#489](https://github.com/nf-core/chipseq/issues/489)]CUSTOM_GETCHROMSIZES was changed to SAMTOOLS_FAIDX instead, since CUSTOM_GETCHROMSIZES is deprecated.
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### Parameters
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### Software dependencies
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Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
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Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own
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[Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the
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pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to
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the last release have been listed below for reference.
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### Software updates
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| | | |
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| | | |
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| macs3 | 3.0.1 | 3.0.4 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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> **NB:** Dependency has been **added** if just the new version information is present.
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> **NB:** Dependency has been **removed** if version information isn't present.
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### Software update local modules
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| Dependency | Old version | New version |
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| --------------------------- | ----------- | ----------- |
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| bamtools | 2.5.2 | 2.5.3 |
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| samtools | 1.15.1 | 1.23 |
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| pysam | 0.19.0 | 0.23.3 |
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| bedtools | 2.30.0 | 2.31.1 |
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| bioconductor-biostrings | 2.58.0 | 2.78.0 |
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| r-base | 4.0.3 | 4.5.3 |
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| r-reshape2 | 1.4.4 | 1.4.5 |
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| r-optparse | 1.6.6 | 1.7.5 |
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| r-ggplot2 | 3.3.3 | 4.0.2 |
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| r-scales | 1.1.1 | 1.4.0 |
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| r-viridis | 0.5.1 | 0.6.5 |
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| r-tidyverse | 1.3.0 | 2.0.0 |
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| bioconductor-complexheatmap | 2.6.2 | 2.26.1 |
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| star | 2.6.1d | 2.7.11b |
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| | | |
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### Local modules refactoring and topic channels update
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| Module | Updated to wave containers | Topic channel added | refactoring (adding .yml files) |
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| ----------------------------------- | -------------------------- | ------------------- | ------------------------------- |
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| annotate_boolean_peaks | | | |
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| bam_remove_orphans | x | x | x |
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| bamtools_filter | x | x | x |
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| deseq2_qc | | | |
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| frip_score | x | x | x |
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| genome_blacklist_regions | x | x | x |
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| gtf2bed | | | |
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| igv | | | |
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| macs3_consensus | x | x | x |
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| multiqc | | | |
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| multiqc_custom_peaks | | | |
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| multiqc_custom_phantompeakqualtools | | | |
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| plot_homer_annotatepeaks | x | x | x |
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| plot_macs3_qc | x | x | x |
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| samplesheet_check | | | |
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| star_align | x | x | x |
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| star_genomegenerate | x | x | x |
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| | | | |
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## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-07
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‎conf/modules.config‎

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]
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}
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withName: 'CUSTOM_GETCHROMSIZES' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'GENOME_BLACKLIST_REGIONS' {
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publishDir = [
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path: { "${params.outdir}/genome" },

‎main.nf‎

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params.chromap_index,
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params.star_index,
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)
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ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
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//
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// WORKFLOW: Run nf-core/chipseq workflow

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