[MODIF] add CALDER2 compartment caller

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+  Add CALDER2 compartments calling (see '--compartments_caller' option)
+
 - Add new '--balancing_opts' to update `cooler balance` arguments
 
 - New subworkflow based on `pairtools` to detect valid pairs. The user

nextflow.config

@@ -90,6 +90,7 @@ params {
     res_dist_decay = '250000'
     tads_caller = 'insulation'
     res_tads = '40000'
+    compartments_caller = 'cooltools'
     res_compartments = '250000'
 
     // Workflow

nextflow_schema.json

@@ -314,6 +314,11 @@
                     "default": "insulation",
                     "description": "Define methods for TADs calling"
                 },
+		"compartments_caller": {
+		    "type": "string",
+		    "default": "cooltools",
+		    "description": "Define methods for compartments calling"
+		},
                 "res_tads": {
                     "type": "string",
                     "pattern": "^(\\d+)(,\\d+)*$",

subworkflows/local/compartments.nf

@@ -1,5 +1,5 @@
 include { COOLTOOLS_EIGSCIS } from '../../modules/local/cooltools/eigscis'
-
+include { CALDER2 } from '../../modules/nfcore/calder2/main'
 workflow COMPARTMENTS {
 
     take:
@@ -10,14 +10,26 @@ workflow COMPARTMENTS {
     main:
     ch_versions = Channel.empty()
 
-    COOLTOOLS_EIGSCIS(
-        cool,
-        fasta.map{it -> it[1]}.collect(),
-        chrsize.map{it -> it[1]}.collect()
-    )
-    ch_versions = ch_versions.mix(COOLTOOLS_EIGSCIS.out.versions)
+    if (params.compartments_caller =~ 'cooltools'){
+        COOLTOOLS_EIGSCIS(
+            cool,
+            fasta.map{it -> it[1]}.collect(),
+            chrsize.map{it -> it[1]}.collect()
+        )
+        ch_versions = ch_versions.mix(COOLTOOLS_EIGSCIS.out.versions)
+        ch_comp = COOLTOOLS_EIGSCIS.out.results	
+    }
+
+    if (params.compartments_caller =~ 'calder2'){
+        CALDER2(
+            cool,
+            Channel.value([])
+        )
+        ch_versions = ch_versions.mix(CALDER2.out.versions
+        ch_comp = CALDER2.out.output_folder
+    }
 
     emit:
     versions = ch_versions
-    compartments = COOLTOOLS_EIGSCIS.out.results
+    compartments = ch_comp
 }