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Merged
Kevin-Brockers merged 10 commits into from
Jul 22, 2026
Merged

Update homer/annoatepeaks to topic channels #530

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b3a638f
Update homer/annotatepeaks
JoseEspinosa Jul 15, 2026
4ebc8f9
Update subworkflows using homer/annotatepeaks
JoseEspinosa Jul 15, 2026
eba5a35
Update snapshots
JoseEspinosa Jul 15, 2026
5a75fdb
Update changelog
JoseEspinosa Jul 15, 2026
4a70479
Merge branch 'dev' into fixes
JoseEspinosa Jul 15, 2026
161e14e
Change 'conda' to 'container' for FASTQC process
Kevin-Brockers Jul 16, 2026
d3a203e
Change 'conda' to 'container' for FASTQC process
Kevin-Brockers Jul 16, 2026
f4dfb3d
Update nf-test for start
JoseEspinosa Jul 16, 2026
b07bb28
Merge branch 'fixes' of https://github.com/JoseEspinosa/chipseq into …
JoseEspinosa Jul 16, 2026
4b314f6
Merge branch 'dev' into fixes
Kevin-Brockers Jul 21, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2).
- [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`.
- [[#456] (https://github.com/nf-core/chipseq/issues/456)] - Use `--skip_preseq` by default.
- [[#530] (https://github.com/nf-core/chipseq/issues/456)] - Update `hommer/annotatepeaks` to topic channels.
- [[#531] (https://github.com/nf-core/chipseq/issues/531)] - Changed chromap decompression - untarfiles (depreciated) to untar modules

### Parameters
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -78,7 +78,7 @@
},
"homer/annotatepeaks": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "9ed7f157dd96f83b852da7ea4d3a217907f50f36",
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
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19 changes: 3 additions & 16 deletions modules/nf-core/homer/annotatepeaks/main.nf
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29 changes: 22 additions & 7 deletions modules/nf-core/homer/annotatepeaks/meta.yml
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9 changes: 2 additions & 7 deletions modules/nf-core/homer/annotatepeaks/tests/main.nf.test
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71 changes: 37 additions & 34 deletions modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap
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3 changes: 0 additions & 3 deletions subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
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Expand Up @@ -26,8 +26,6 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {

main:

ch_versions = channel.empty()

//
// Call peaks with MACS3
//
Expand Down Expand Up @@ -98,7 +96,6 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
ch_gtf
)
ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt
ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first())

if (!skip_peak_qc) {
//
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2 changes: 0 additions & 2 deletions subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf
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Expand Up @@ -23,8 +23,6 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {

main:

ch_versions = channel.empty()

// Create channels: [ meta , [ peaks ] ]
// Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
ch_peaks
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10 changes: 7 additions & 3 deletions tests/bowtie2.nf.test.snap
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Expand Up @@ -53,6 +53,9 @@
"GTF2BED": {
"perl": "5.26.2"
},
"HOMER_ANNOTATEPEAKS": {
"homer": 4.11
},
"IGV": {
"python": "3.12.12"
},
Expand Down Expand Up @@ -948,9 +951,10 @@
],
"timestamp": "2026-07-21T12:38:39.799024",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-07-15T22:14:42.929516361"
},
"bowtie2 with stub": {
"content": [
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10 changes: 7 additions & 3 deletions tests/chromap.nf.test.snap
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Expand Up @@ -49,6 +49,9 @@
"GTF2BED": {
"perl": "5.26.2"
},
"HOMER_ANNOTATEPEAKS": {
"homer": 4.11
},
"IGV": {
"python": "3.12.12"
},
Expand Down Expand Up @@ -953,9 +956,10 @@
],
"timestamp": "2026-07-21T12:49:50.568622",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-07-15T22:31:46.117520522"
},
"chromap with stub": {
"content": [
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10 changes: 7 additions & 3 deletions tests/default.nf.test.snap
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Expand Up @@ -52,6 +52,9 @@
"GTF2BED": {
"perl": "5.26.2"
},
"HOMER_ANNOTATEPEAKS": {
"homer": 4.11
},
"IGV": {
"python": "3.12.12"
},
Expand Down Expand Up @@ -947,8 +950,9 @@
],
"timestamp": "2026-07-21T13:00:00.044632",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-07-15T22:47:34.878161789"
}
}
10 changes: 7 additions & 3 deletions tests/skip_consensus_peaks.nf.test.snap
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Expand Up @@ -55,6 +55,9 @@
"GTF2BED": {
"perl": "5.26.2"
},
"HOMER_ANNOTATEPEAKS": {
"homer": 4.11
},
"IGV": {
"python": "3.12.12"
},
Expand Down Expand Up @@ -888,8 +891,9 @@
],
"timestamp": "2026-07-21T13:09:28.447257",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-07-15T23:01:54.394780524"
}
}
10 changes: 7 additions & 3 deletions tests/skip_trimming.nf.test.snap
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Expand Up @@ -52,6 +52,9 @@
"GTF2BED": {
"perl": "5.26.2"
},
"HOMER_ANNOTATEPEAKS": {
"homer": 4.11
},
"IGV": {
"python": "3.12.12"
},
Expand Down Expand Up @@ -825,9 +828,10 @@
],
"timestamp": "2026-07-21T13:19:06.842802",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
"nf-test": "0.9.3",
"nextflow": "26.04.1"
},
"timestamp": "2026-07-15T23:17:15.190122205"
},
"skip_trimming with stub": {
"content": [
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