Pull request for adding compartmentalization analysis

.github/workflows/linting.yml

@@ -32,6 +32,8 @@ jobs:
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
+        with:
+          version: "25.10.4"
 
       - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:

.nf-core.yml

@@ -1,6 +1,8 @@
 lint:
   multiqc_config:
     - report_comment
+  files_unchanged:
+    - .github/workflows/linting.yml
 nf_core_version: 3.4.1
 repository_type: pipeline
 template:

CITATIONS.md

@@ -64,6 +64,10 @@
 
   > Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. Biotech. doi:10.1038/nbt.1508
 
+- [CALDER2](https://github.com/CSOgroup/CALDER2)
+
+  > Liu, Y., Nanni, L., Sungalee, S. et al. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nat Commun 12, 2439 (2021). doi:10.1038/s41467-021-22666-3
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -38,9 +38,10 @@ Here is an outline of the analysis steps:
 4. Mark duplicate reads ([`picard Markduplicates`](http://broadinstitute.github.io/picard))
 5. Filter reads and generate alignment statistics ([`samtools`](http://www.htslib.org/))
 6. Create single track profiles in bigwig format ([`deeptools bamCoverage`](https://deeptools.readthedocs.io/en/latest/))
-7. (Optional) Generate pairwise comparison tracks in bigWig format ([`spp`](https://github.com/hms-dbmi/spp)) or ([`deeptools bigwigCompare`](https://deeptools.readthedocs.io/en/develop/content/tools/bigwigCompare.html)).
-8. (Optional) Identify differentially enriched solubility regions as described in [Wang et al., 2024 ](https://doi.org/10.1038/s41594-025-01622-5).
-9. Generate an analysis report by collecting all generated QC and statistics ([`MultiQC`](http://multiqc.info/))
+7. (Optional) Perform chromatin compartmentalization analysis to identify A/B compartments across chromosomes ([`CALDER2`](https://github.com/CSOgroup/CALDER2)).
+8. (Optional) Generate pairwise comparison tracks in bigWig format ([`spp`](https://github.com/hms-dbmi/spp)) or ([`deeptools bigwigCompare`](https://deeptools.readthedocs.io/en/develop/content/tools/bigwigCompare.html)).
+9. (Optional) Identify differentially enriched solubility regions as described in [Wang et al., 2025 ](https://doi.org/10.1038/s41594-025-01622-5).
+10. Generate an analysis report by collecting all generated QC and statistics ([`MultiQC`](http://multiqc.info/))
 
 <p align="center">
     <img title="sammyseq scheme" src="docs/images/nf-core-sammyseq_tubemap.png" width=100%>