nf-core · LouisLeNezet · Nov 18, 2025 · Nov 18, 2025 · Nov 18, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#188](https://github.com/nf-core/phaseimpute/pull/188) - Add documentation for all subworkflows.
 - [#210](https://github.com/nf-core/phaseimpute/pull/200) - Add BEAGLE5 support for genotype imputation.
 - [#211](https://github.com/nf-core/phaseimpute/pull/211) - Add MINIMAC4 support for genotype imputation.
+- [#219](https://github.com/nf-core/phaseimpute/pull/219) - Add genetic map support for `QUILT`.
 
 ### `Changed`
 

diff --git a/subworkflows/local/bam_impute_quilt/main.nf b/subworkflows/local/bam_impute_quilt/main.nf
@@ -8,27 +8,24 @@ workflow BAM_IMPUTE_QUILT {
     ch_hap_legend        // channel: [ [panel, chr], hap, legend ]
     ch_chunks            // channel: [ [panel, chr], chr, start_coordinate, end_coordinate ]
     ch_fasta             // channel: [ [genome], fa, fai ]
+    ch_map               // channel: [ [chr], genetic_map ]
 
     main:
 
-    ch_versions = Channel.empty()
-
-    genetic_map_file    = []
+    ch_versions = channel.empty()
 
     ngen_params         = params.ngen
     buffer_params       = params.buffer
 
     ch_hap_chunks = ch_hap_legend
         .combine(ch_chunks, by:0)
-        .map { it + ngen_params + buffer_params + [[]] }
-
-    if (!genetic_map_file.isEmpty()) {
-        // Add genetic map file (untested)
-        ch_hap_chunks = ch_hap_chunks
-            .map{it[0..-1]}
-            .join(genetic_map_file)
-    }
-
+        .map{ metaPC, hap, legend, chr, start, end ->
+            [metaPC.subMap("chr"), metaPC, hap, legend, chr, start, end]
+        }
+        .combine(ch_map, by:0)
+        .map{ _metaC, metaPC, hap, legend, chr, start, end, map ->
+            [metaPC, hap, legend, chr, start, end, ngen_params, buffer_params, map]
+        }
     ch_quilt = ch_input
         .combine(ch_hap_chunks)
         .map {
@@ -46,7 +43,7 @@ workflow BAM_IMPUTE_QUILT {
     // Annotate the variants
     BCFTOOLS_ANNOTATE(QUILT_QUILT.out.vcf
         .join(QUILT_QUILT.out.tbi)
-        .combine(Channel.of([[], [], [], []]))
+        .combine(channel.of([[], [], [], []]))
     )
     ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions.first())
 

diff --git a/subworkflows/local/bam_impute_quilt/meta.yml b/subworkflows/local/bam_impute_quilt/meta.yml
@@ -83,6 +83,18 @@ input:
           type: file
           description: FASTA index file of the reference genome
           pattern: "*.fai"
+  - ch_map:
+      description: Channel with genetic map data
+      structure:
+        - meta:
+          type: map
+          description: |
+            Metadata map containing chromosome information
+            Need to have "chr" as chromosome name
+        - map:
+          type: file
+          description: Stitch format genetic map files
+          pattern: "*.map"
 output:
   - vcf_tbi:
       description: Channel with imputed VCF files

diff --git a/subworkflows/local/bam_impute_quilt/tests/main.nf.test b/subworkflows/local/bam_impute_quilt/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
     tag "bcftools/index"
     tag "bcftools/annotate"
 
-    test("Impute with quilt two individuals with bamlist and no renaming") {
+    test("Impute with quilt two individuals with bamlist and no renaming no map") {
         when {
             workflow {
                 """
@@ -52,28 +52,31 @@ nextflow_workflow {
                     [id: "GRCh38"],
                     file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true)
                 ]).collect()
+                input[4] = Channel.of([
+                    [chr: "chr22"], []
+                ])
                 """
             }
         }
         then {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.versions,
                     workflow.out.vcf_tbi.collect{[
                         it[0],
                         path(it[1]).getFileName().toString(),
-                        path(it[2]).getFileName().toString()
-                    ] },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.summary },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.header.getGenotypeSamples().sort() },
+                        path(it[2]).getFileName().toString(),
+                        path(it[1]).vcf.summary,
+                        path(it[1]).vcf.header.getGenotypeSamples().sort(),
+                        path(it[1]).vcf.variantsMD5
+                    ]},
                     workflow.out.versions.collect{ path(it).yaml }
                 ).match() }
             )
         }
     }
 
-    test("Impute with quilt two individuals with bamlist and renaming") {
+    test("Impute with quilt two individuals with bamlist and renaming no map") {
         when {
             workflow {
                 """
@@ -112,6 +115,9 @@ nextflow_workflow {
                     [id: "GRCh38"],
                     file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true)
                 ]).collect()
+                input[4] = Channel.of([
+                    [chr: "chr22"], []
+                ])
                 """
             }
         }
@@ -120,21 +126,21 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.versions,
                     workflow.out.vcf_tbi.collect{[
                         it[0],
                         path(it[1]).getFileName().toString(),
-                        path(it[2]).getFileName().toString()
-                    ] },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.summary },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.header.getGenotypeSamples().sort() },
+                        path(it[2]).getFileName().toString(),
+                        path(it[1]).vcf.summary,
+                        path(it[1]).vcf.header.getGenotypeSamples().sort(),
+                        path(it[1]).vcf.variantsMD5
+                    ]},
                     workflow.out.versions.collect{ path(it).yaml }
                 ).match() }
             )
         }
     }
 
-    test("Impute with quilt one individuals") {
+    test("Impute with quilt one individuals with map") {
         when {
             workflow {
                 """
@@ -160,6 +166,10 @@ nextflow_workflow {
                     [id: "GRCh38"],
                     file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true)
                 ]).collect()
+                input[4] = Channel.of([
+                    [chr: "chr22"],
+                    file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.stitch.map", checkIfExist:true)
+                ])
                 """
             }
         }
@@ -168,14 +178,15 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out.versions,
                     workflow.out.vcf_tbi.collect{[
                         it[0],
                         path(it[1]).getFileName().toString(),
-                        path(it[2]).getFileName().toString()
-                    ] },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.summary },
-                    workflow.out.vcf_tbi.collect{ path(it[1]).vcf.header.getGenotypeSamples().sort() }
+                        path(it[2]).getFileName().toString(),
+                        path(it[1]).vcf.summary,
+                        path(it[1]).vcf.header.getGenotypeSamples().sort(),
+                        path(it[1]).vcf.variantsMD5
+                    ]},
+                    workflow.out.versions.collect{ path(it).yaml }
                 ).match() }
             )
         }