Set params.chunk_model

nf-core · Nov 8, 2024 · 7a5938b · 7a5938b
1 parent ca6c5a5
commit 7a5938b
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Showing 10 changed files with 24 additions and 12 deletions.
diff --git a/conf/test_all.config b/conf/test_all.config
@@ -33,6 +33,7 @@ params {
     phase        = true
     normalize    = true
     compute_freq = false
+    chunk_model  = "recursive"
 
     // Pipeline steps
     steps = "all"

diff --git a/conf/test_dog.config b/conf/test_dog.config
@@ -32,6 +32,7 @@ params {
     normalize    = false
     compute_freq = false
     rename_chr   = true
+    chunk_model  = "recursive"
 
     // Input data
     input        = params.pipelines_testdata_base_path + "dog_data/csv/sample_dog.csv"

diff --git a/conf/test_panelprep.config b/conf/test_panelprep.config
@@ -32,6 +32,7 @@ params {
     normalize      = true
     compute_freq   = true
     remove_samples = "HG00096,HG00097,HG00099,HG00100"
+    chunk_model    = "recursive"
 
     // Pipeline steps
     steps   = "panelprep"

diff --git a/nextflow.config b/nextflow.config
@@ -10,7 +10,7 @@
 params {
 
     // steps
-    steps                        = null
+    steps                       = null
 
     // Input options
     input                       = null
@@ -24,6 +24,7 @@ params {
     normalize                   = true
     compute_freq                = false
     remove_samples              = null
+    chunk_model                 = 'sequential'
 
     // ChrCheck parameters
     rename_chr                  = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -132,6 +132,13 @@
                 "binaryref": {
                     "type": "string",
                     "description": "Whether to generate a binary reference file to be used with GLIMPSE2"
+                },
+                "chunk_model" : {
+                    "type": "string",
+                    "description": "Model type to use for GLIMPSE2_CHUNK",
+                    "enum": ["recursive", "sequential", "uniform-number-variants"],
+                    "default": "sequential",
+                    "hidden": true
                 }
             }
         },

diff --git a/subworkflows/local/vcf_chunk_glimpse/main.nf b/subworkflows/local/vcf_chunk_glimpse/main.nf
@@ -7,6 +7,7 @@ workflow VCF_CHUNK_GLIMPSE {
     take:
     ch_reference  // channel: [ [panel, chr], vcf, csi ]
     ch_map        // channel  (optional): [ [chr], map ]
+    chunk_model   // channel : model
 
     main:
 
@@ -36,9 +37,6 @@ workflow VCF_CHUNK_GLIMPSE {
         )
         .map { metaPC, it -> [metaPC, it["RegionIn"], it["RegionOut"]]}
 
-    // Make chunks with Glimpse2 (does not work with "sequential" mode)
-    chunk_model = "recursive"
-
     ch_input_glimpse2 = ch_vcf_csi_chr
         .map{
             metaPC, vcf, csi, chr -> [metaPC.subMap("chr"), metaPC, vcf, csi, chr]

diff --git a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
@@ -47,6 +47,7 @@ nextflow_workflow {
                         file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_21.map", checkIfExist:true)
                     ]
                 )
+                input[2] = "recursive"
                 """
             }
         }
@@ -87,6 +88,7 @@ nextflow_workflow {
                     [[chr: "chr22"], []],
                     [[chr: "chr21"], []]
                 )
+                input[2] = "recursive"
                 """
             }
         }

diff --git a/subworkflows/local/vcf_phase_shapeit5/main.nf b/subworkflows/local/vcf_phase_shapeit5/main.nf
@@ -7,19 +7,17 @@ include { BCFTOOLS_INDEX as VCF_BCFTOOLS_INDEX_2 } from '../../../modules/nf-cor
 workflow VCF_PHASE_SHAPEIT5 {
 
     take:
-    ch_vcf        // channel (mandatory): [ [id, chr], vcf, csi, pedigree ]
+    ch_vcf        // channel (mandatory) : [ [id, chr], vcf, csi, pedigree ]
     ch_region     // channel (mandatory) : [ [chr, region], region ]
-    ch_ref        // channel (optional) : [ [id, chr], ref, csi ]
-    ch_scaffold   // channel (optional) : [ [id, chr], scaffold, csi ]
+    ch_ref        // channel (optional)  : [ [id, chr], ref, csi ]
+    ch_scaffold   // channel (optional)  : [ [id, chr], scaffold, csi ]
     ch_map        // channel (mandatory) : [ [chr], map]
+    chunk_model   // channel (mandatory) : [ model ]
 
     main:
 
     ch_versions = Channel.empty()
 
-    // Make chunks with Glimpse2 (does not work with "sequential" mode)
-    chunk_model = "recursive"
-
     // Chunk with Glimpse2
     ch_input_glimpse2 = ch_vcf
         .map{

diff --git a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test
@@ -52,6 +52,7 @@ nextflow_workflow {
                     [[chr: "chr22"],[]],
                     [[chr: "chr21"], []]
                 )
+                input[5] = "recursive"
                 """
             }
         }
@@ -109,6 +110,7 @@ nextflow_workflow {
                     [ [chr: "chr22"], file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_22.map", checkIfExist:true)],
                     [ [chr: "chr21"], file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_21.map", checkIfExist:true)]
                 )
+                input[5] = "recursive"
                 """
             }
         }

diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
@@ -171,14 +171,15 @@ workflow PHASEIMPUTE {
                 ch_region,
                 [[],[],[]],
                 [[],[],[]],
-                ch_map
+                ch_map,
+                params.chunk_model
             )
             ch_panel_phased = VCF_PHASE_SHAPEIT5.out.vcf_tbi
             ch_versions = ch_versions.mix(VCF_PHASE_SHAPEIT5.out.versions)
         }
 
         // Create chunks from reference VCF
-        VCF_CHUNK_GLIMPSE(ch_panel_phased, ch_map)
+        VCF_CHUNK_GLIMPSE(ch_panel_phased, ch_map, params.chunk_model)
         ch_versions = ch_versions.mix(VCF_CHUNK_GLIMPSE.out.versions)
 
         // Assign chunks channels