nf-core · JoseEspinosa · Mar 19, 2026 · Mar 11, 2026 · Mar 11, 2026 · Mar 11, 2026
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,9 +1,13 @@
 lint:
+  files_unchanged:
+    - assets/nf-core-chipseq_logo_light.png
+    - docs/images/nf-core-chipseq_logo_dark.png
+    - docs/images/nf-core-chipseq_logo_light.png
   nextflow_config:
     - config_defaults:
         - params.bamtools_filter_se_config
         - params.bamtools_filter_pe_config
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.
 - [[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)
 - [[#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.
+- [[#484](https://github.com/nf-core/chipseq/issues/484)] - Updated modules and subworkflows
+- [[#483]] - Updated nf-core related things to topics, still a few nf-core modules are pending and the local modules
+  need to be fixed.
+- CUSTOM_GETCGRINSIZES was switcht to SAMTOOLS_FAIDX
+
 
 ### Parameters
 

diff --git a/assets/nf-core-chipseq_logo_light.png b/assets/nf-core-chipseq_logo_light.png
diff --git a/docs/images/nf-core-chipseq_logo_dark.png b/docs/images/nf-core-chipseq_logo_dark.png
diff --git a/main.nf b/main.nf
@@ -33,9 +33,9 @@ params.macs_gsize    = getMacsGsize(params)
 */
 
 include { CHIPSEQ                 } from './workflows/chipseq'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome/main'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_chipseq_pipeline/main'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_chipseq_pipeline/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -66,7 +66,6 @@ workflow NFCORE_CHIPSEQ {
         params.chromap_index,
         params.star_index,
     )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
     // WORKFLOW: Run nf-core/chipseq workflow

diff --git a/modules.json b/modules.json
@@ -7,179 +7,179 @@
                 "nf-core": {
                     "bedtools/genomecov": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
+                        "git_sha": "92b8df948fd8cdb223e051f5f5e414818a073ee0",
                         "installed_by": ["fastq_align_bowtie2", "modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
+                        "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
+                        "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef",
                         "installed_by": ["fastq_align_bwa", "modules"]
                     },
                     "chromap/chromap": {
                         "branch": "master",
-                        "git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["fastq_align_chromap", "modules"],
                         "patch": "modules/nf-core/chromap/chromap/chromap-chromap.diff"
                     },
                     "chromap/index": {
                         "branch": "master",
-                        "git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
-                        "installed_by": ["modules"]
-                    },
-                    "custom/getchromsizes": {
-                        "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "deeptools/computematrix": {
                         "branch": "master",
-                        "git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
+                        "git_sha": "b985685ece5113213a0ad282da9f93c40dfe7119",
                         "installed_by": ["modules"]
                     },
                     "deeptools/plotfingerprint": {
                         "branch": "master",
-                        "git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
+                        "git_sha": "b985685ece5113213a0ad282da9f93c40dfe7119",
                         "installed_by": ["modules"]
                     },
                     "deeptools/plotheatmap": {
                         "branch": "master",
-                        "git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
+                        "git_sha": "b985685ece5113213a0ad282da9f93c40dfe7119",
                         "installed_by": ["modules"]
                     },
                     "deeptools/plotprofile": {
                         "branch": "master",
-                        "git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
+                        "git_sha": "b985685ece5113213a0ad282da9f93c40dfe7119",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
+                        "git_sha": "51f2b493a7ff28b40a9f99faca64245521f2bb24",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "96c57dfd98a0641886a67bd449fe33ee2ec0e374",
                         "installed_by": ["modules"]
                     },
                     "homer/annotatepeaks": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "khmer/uniquekmers": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "macs3/callpeak": {
                         "branch": "master",
-                        "git_sha": "3a3f471ed42f640115b2661edee5b258e6a254c1",
+                        "git_sha": "fe0ec4b67b1abd71ff9b5ece41fd5a4d8abadad5",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
                         "installed_by": ["modules"]
                     },
                     "phantompeakqualtools": {
                         "branch": "master",
-                        "git_sha": "ec48f56f6e1571e23800aaaba41cceda13408e02",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
-                        "git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["bam_markduplicates_picard", "modules"]
                     },
                     "picard/mergesamfiles": {
                         "branch": "master",
-                        "git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "preseq/lcextrap": {
                         "branch": "master",
-                        "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
+                        "git_sha": "b80fa93d646109e3dc86e79010bf7c0b0af8ce29",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["bam_stats_samtools", "modules"],
                         "patch": "modules/nf-core/samtools/flagstat/samtools-flagstat.diff"
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "git_sha": "95cc6bff05f02c53ac9478f7b8d749969c514fca",
                         "installed_by": ["modules"]
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "git_sha": "eed5d14302a6c9070dcc25feeab707a27a4b3254",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "b1c64e862fb5ed7f13b6f8f3ef8f04e700d41438",
                         "installed_by": ["modules"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "git_sha": "bd6d730b3f32742f402189113ba9480006a3350f",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "untarfiles": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "bc71bfe17a9c2057f1781b5b16987dcc14d1063f",
                         "installed_by": ["modules"]
                     }
                 }
@@ -188,37 +188,37 @@
                 "nf-core": {
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "7ac6cbe7c17c2dad685da7f70496c8f48ea48687",
                         "installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "git_sha": "7ac6cbe7c17c2dad685da7f70496c8f48ea48687",
                         "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
                     },
                     "fastq_align_bowtie2": {
                         "branch": "master",
-                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_bwa": {
                         "branch": "master",
-                        "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
+                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_chromap": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "8f2ec534d0418bf724cfd5f053176a9c500fae78",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -228,12 +228,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/local/annotate_boolean_peaks.nf → modules/local/annotate_boolean_peaks/main.nf b/modules/local/annotate_boolean_peaks.nf → modules/local/annotate_boolean_peaks/main.nf
diff --git a/modules/local/bam_remove_orphans.nf → modules/local/bam_remove_orphans/main.nf b/modules/local/bam_remove_orphans.nf → modules/local/bam_remove_orphans/main.nf
diff --git a/modules/local/bamtools_filter.nf → modules/local/bamtools_filter/main.nf b/modules/local/bamtools_filter.nf → modules/local/bamtools_filter/main.nf
diff --git a/modules/local/deseq2_qc.nf → modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc.nf → modules/local/deseq2_qc/main.nf
diff --git a/modules/local/frip_score.nf → modules/local/frip_score/main.nf b/modules/local/frip_score.nf → modules/local/frip_score/main.nf
diff --git a/modules/local/genome_blacklist_regions.nf → ...es/local/genome_blacklist_regions/main.nf b/modules/local/genome_blacklist_regions.nf → ...es/local/genome_blacklist_regions/main.nf
diff --git a/modules/local/gtf2bed.nf → modules/local/gtf2bed/main.nf b/modules/local/gtf2bed.nf → modules/local/gtf2bed/main.nf
diff --git a/modules/local/igv.nf → modules/local/igv/main.nf b/modules/local/igv.nf → modules/local/igv/main.nf
diff --git a/modules/local/macs3_consensus.nf → modules/local/macs3_consensus/main.nf b/modules/local/macs3_consensus.nf → modules/local/macs3_consensus/main.nf
diff --git a/modules/local/multiqc.nf → modules/local/multiqc/main.nf b/modules/local/multiqc.nf → modules/local/multiqc/main.nf
diff --git a/modules/local/multiqc_custom_peaks.nf → modules/local/multiqc_custom_peaks/main.nf b/modules/local/multiqc_custom_peaks.nf → modules/local/multiqc_custom_peaks/main.nf
diff --git a/...al/multiqc_custom_phantompeakqualtools.nf → ...ltiqc_custom_phantompeakqualtools/main.nf b/...al/multiqc_custom_phantompeakqualtools.nf → ...ltiqc_custom_phantompeakqualtools/main.nf
diff --git a/modules/local/plot_homer_annotatepeaks.nf → ...es/local/plot_homer_annotatepeaks/main.nf b/modules/local/plot_homer_annotatepeaks.nf → ...es/local/plot_homer_annotatepeaks/main.nf
diff --git a/modules/local/plot_macs3_qc.nf → modules/local/plot_macs3_qc/main.nf b/modules/local/plot_macs3_qc.nf → modules/local/plot_macs3_qc/main.nf
diff --git a/modules/local/samplesheet_check.nf → modules/local/samplesheet_check/main.nf b/modules/local/samplesheet_check.nf → modules/local/samplesheet_check/main.nf
diff --git a/modules/local/star_align.nf → modules/local/star_align/main.nf b/modules/local/star_align.nf → modules/local/star_align/main.nf
diff --git a/modules/local/star_genomegenerate.nf → modules/local/star_genomegenerate/main.nf b/modules/local/star_genomegenerate.nf → modules/local/star_genomegenerate/main.nf