Add haplotype DMR (differential methylation region) calling

conf/igenomes.config

@@ -24,6 +24,8 @@ params.genomes = [
         vep_species     : "homo_sapiens",
         savana_contigs   : "https://raw.githubusercontent.com/cortes-ciriano-lab/savana/main/example/contigs.chr.hg38.txt",
         savana_g1000_vcf : "1000g_hg38",
+        dmr_cpg_islands_bed  : "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/dmr/GRCh38.cpg_islands.bed.gz",
+        dmr_gencode_gene_bed : "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/dmr/GRCh38.gencode_gene.bed.gz",
         vep_alphamissense        : "https://storage.googleapis.com/dm_alphamissense/AlphaMissense_hg38.tsv.gz",
         vep_alphamissense_tbi    : "https://g-608c0c.273595.03c0.data.globus.org/VEP_plugins/AlphaMissense_hg38.tsv.gz.tbi",
         // A dated release rather than the rolling vcf_GRCh38/clinvar.vcf.gz, whose VCF and
@@ -54,6 +56,8 @@ params.genomes = [
         vep_species     : "homo_sapiens_gca009914755v4",
         savana_contigs   : "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/savana/contigs.chr.chm13.txt",
         savana_g1000_vcf : "1000g_t2t",
+        dmr_cpg_islands_bed  : "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/dmr/CHM13.cpg_islands.bed.gz",
+        dmr_gencode_gene_bed : "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/dmr/CHM13.gencode_gene.bed.gz",
         vep_alphamissense_aa     : "https://g-608c0c.273595.03c0.data.globus.org/VEP_plugins/alphamissense_protein_v2023_uniprot-2026_03.tsv.gz",
         vep_alphamissense_aa_tbi : "https://g-608c0c.273595.03c0.data.globus.org/VEP_plugins/alphamissense_protein_v2023_uniprot-2026_03.tsv.gz.tbi",
         // Pinned to a release rather than current_variation/, which moves at every Ensembl release

conf/modules.config

@@ -345,6 +345,40 @@ process {
         ]
     }
 
+    //
+    // SUBWORKFLOW: DMR -- intermediate steps (tabix-indexing, CpG-island restriction, the raw
+    // modkit dmr pair output) are not published; DMR_NEAREST_GENE's annotated bed is the final
+    // deliverable.
+    //
+    withName: '.*:DMR:HTSLIB_BGZIPTABIX' {
+        // meta.haplotype ('hp1'/'hp2') is stripped from meta again right after this step (both
+        // haplotypes are rejoined under the plain sample meta), so it has to be in the filename
+        // instead -- otherwise hp1 and hp2 both stage as <sample>.bed.gz into DMR_HAPLOTYPE_REGIONS.
+        ext.prefix = { "${meta.id}_${meta.haplotype}" }
+        ext.args2 = '-p bed'
+        publishDir = [
+            enabled: false
+        ]
+    }
+    withName: '.*:DMR:DMR_HAPLOTYPE_REGIONS' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+    withName: '.*:DMR:MODKIT_DMR' {
+        ext.args = '--base C'
+        publishDir = [
+            enabled: false
+        ]
+    }
+    withName: '.*:DMR:DMR_NEAREST_GENE' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}/methylation/${meta.type}/dmr" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: '.*:FIBERTOOLSRS_PREDICTM6A' {
         ext.args = {
             [