Remove binary panel

Author: LouisLeNezet

conf/steps/panel_prep.config

@@ -206,14 +206,4 @@ process {
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_SPLITREFERENCE' {
-        ext.prefix    = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
-        publishDir = [
-            path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: true
-        ]
-    }
-
 }

modules.json

@@ -113,11 +113,6 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/glimpse2/phase/glimpse2-phase.diff"
                     },
-                    "glimpse2/splitreference": {
-                        "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
-                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/nf-core/glimpse2/splitreference/environment.yml

@@ -69,7 +69,6 @@ params {
     posfile                    = null
 
     // GLIMPSE2
-    binaryref                  = null
     chunks                     = null
 
     // Boilerplate options

modules/nf-core/glimpse2/splitreference/main.nf

@@ -128,10 +128,6 @@
                     "description": "Should the allele frequency for each variant (AC/AN fields necessary for Glimpse1 and the validation step) be computed using VCFFIXUP tool. This can be necessary if the fields are absent from the panel or if samples have been removed.",
                     "type": "boolean"
                 },
-                "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",

modules/nf-core/glimpse2/splitreference/meta.yml

@@ -1,6 +1,5 @@
 include { GLIMPSE_CHUNK           } from '../../../modules/nf-core/glimpse/chunk'
 include { GLIMPSE2_CHUNK          } from '../../../modules/nf-core/glimpse2/chunk'
-include { GLIMPSE2_SPLITREFERENCE } from '../../../modules/nf-core/glimpse2/splitreference'
 
 workflow VCF_CHUNK_GLIMPSE {
 
@@ -29,7 +28,7 @@ workflow VCF_CHUNK_GLIMPSE {
             [metaPC, metaPC.chr, startEnd[0], startEnd[1]]
         }
 
-    // Rearrange chunks into channel for GLIMPSE1
+    // Rearrange chunks into channel for GLIMPSE1 and GLIMPSE2
     ch_chunks_glimpse1 = GLIMPSE_CHUNK.out.chunk_chr
         .splitCsv(
             header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'],
@@ -58,28 +57,10 @@ workflow VCF_CHUNK_GLIMPSE {
         )
         .map { metaPC, it -> [metaPC, it["RegionBuf"], it["RegionCnk"]]}
 
-    // Split reference panel in bin files
-    // Segmentation fault occurs in small-sized panels
-    // Should be run only in full-sized panels
-
-    ch_bins = [[]]
-
-    if (params.binaryref == true) {
-        // Create channel to split reference
-        split_input = ch_reference.join(ch_chunks_glimpse2)
-
-        // Create a binary reference panel for quick reading time
-        GLIMPSE2_SPLITREFERENCE( split_input, ch_map )
-        ch_versions = ch_versions.mix( GLIMPSE2_SPLITREFERENCE.out.versions.first() )
-
-        ch_bins = GLIMPSE2_SPLITREFERENCE.out.bin_ref
-    }
-
     emit:
     chunks                    = GLIMPSE_CHUNK.out.chunk_chr           // channel:  [ [panel, chr], txt ]
     chunks_quilt              = ch_chunks_quilt                       // channel:  [ [panel, chr], chr,  start, end ]
     chunks_glimpse1           = ch_chunks_glimpse1                    // channel:  [ [panel, chr], chr,  region1, region2 ]
-    chunks_glimpse2           = ch_chunks_glimpse2                    // channel:  [ [panel, chr], chr,  region1, region2 ]
-    binary                    = ch_bins                               // channel:  [ [panel, chr], bin]
+    chunks_glimpse2           = ch_chunks_glimpse2                    // channel:  [ [panel, chr], chr,  region1, region2 ]                              // channel:  [ [panel, chr], bin]
     versions                  = ch_versions                           // channel:  [ versions.yml ]
 }