From b36bc45877181079644572a8509465ec47cf57d7 Mon Sep 17 00:00:00 2001
From: Judith Ballesteros <judith.vballesteros@gmail.com>
Date: Fri, 26 Jan 2024 12:03:04 +0100
Subject: [PATCH] trying to add bed from reference file

---
 ...ermination.nf => run_sex_determination.nf} | 30 ++++++++++----
 workflows/eager.nf                            | 41 +++++--------------
 2 files changed, 32 insertions(+), 39 deletions(-)
 rename subworkflows/local/{sex_determination.nf => run_sex_determination.nf} (59%)

diff --git a/subworkflows/local/sex_determination.nf b/subworkflows/local/run_sex_determination.nf
similarity index 59%
rename from subworkflows/local/sex_determination.nf
rename to subworkflows/local/run_sex_determination.nf
index b20c9cdd7..e522bf9db 100644
--- a/subworkflows/local/sex_determination.nf
+++ b/subworkflows/local/run_sex_determination.nf
@@ -20,21 +20,33 @@ workflow RUN_SEXDETERMINE {
     // Generate sex_determine input
     // Break here the input not in the workflow
 
-    ch_samtoolsdepth_input = sexdeterrmine_bam
-                            .combine(sexdeterrmine_bed)
-                            .multiMap{
-                            meta, bam, meta2, bed ->
-                            bam       : [ meta, bam ]
-                            intervals : [ meta2, bed ]
-                                    }
+    ch_bed = sexdeterrmine_bed
+        .map {
+            // Prepend a new meta that contains the meta.id value as the new_meta.reference attribute
+            WorkflowEager.addNewMetaFromAttributes( it, "id" , "reference" , false )
+        }
+
+    ch_input_sexdetermine = sexdeterrmine_bam
+        .map {
+            // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
+            WorkflowEager.addNewMetaFromAttributes( it, "reference" , "reference" , false )
+        }
+        .combine( ch_bed, by: 0 ) // [ [combine_meta], [meta], bam, bai, [ref_meta], bed ]
+
+    ch_samtoolsdepth_input = ch_input_sexdetermine
+            .multiMap {
+                ignore_me, meta, bam, bai, ref_meta, bed ->
+                    bam: [ meta, bam ]
+                    bed: [ ref_meta, bed ]
+            }
 
     SAMTOOLS_DEPTH_SEXDETERMINE(ch_samtoolsdepth_input)
     ch_sex_determine_input = SAMTOOLS_DEPTH_SEXDETERMINE.out.tsv
     ch_versions            = ch_versions.mix( SAMTOOLS_DEPTH_SEXDETERMINE.out.versions )
 
     // Run sex determination with samtools depth input
-    // Does it need a sample list file to run?
-    SEXDETERRMINE(ch_sex_determine_input, sexdeterrmine_list)
+    // Does it need a sample list file to run? yep
+    SEXDETERRMINE(ch_sex_determine_input)
     ch_coverages          = SEXDETERRMINE.out.tsv
     ch_multiqc_files      = ch_multiqc_files.mix( SEXDETERRMINE.out.json )
     ch_versions           = ch_versions.mix( SEXDETERRMINE.out.versions )
diff --git a/workflows/eager.nf b/workflows/eager.nf
index 7e09d1bf8..5aa4f89dd 100644
--- a/workflows/eager.nf
+++ b/workflows/eager.nf
@@ -71,7 +71,7 @@ include { MANIPULATE_DAMAGE             } from '../subworkflows/local/manipulate
 include { METAGENOMICS_COMPLEXITYFILTER } from '../subworkflows/local/metagenomics_complexityfilter'
 include { ESTIMATE_CONTAMINATION        } from '../subworkflows/local/estimate_contamination'
 include { CALCULATE_DAMAGE              } from '../subworkflows/local/calculate_damage'
-include { RUN_SEXDETERMINE              } from '../subworkflows/local/sex_determination'
+include { RUN_SEXDETERMINE              } from '../subworkflows/local/run_sex_determination'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -134,25 +134,12 @@ workflow EAGER {
     }
 
 
-    // Sex determine
+    // SUBWORKFLOW: Run Sex determination
     if ( params.sexdeterrmine_bedfile ) {
-      ch_sexdeterrmine_bed = Channel.fromPath( params.sexdeterrmine_bedfile, checkIfExists: true )
-        .collect()
-        .map {
-          file ->
-              meta = file.simpleName
-          [meta,file]
-        }
-
-    } else {
-      ch_sexdeterrmine_bed = []
-    }
-
-    if ( params.sexdeterrmine_samplelist) {
-      ch_sexdeterrmine_samplelist = Channel.fromPath( params.sexdeterrmine_samplelist, checkIfExists: true )
-
-    } else {
-      ch_sexdeterrmine_samplelist = []
+      ch_sexdeterrmine_bed = REFERENCE_INDEXING.out.sexdeterrmine_bed
+            .map{
+                WorkflowEager.addNewMetaFromAttributes( it, "id" , "reference" , false )
+            }
     }
 
     //
@@ -534,21 +521,15 @@ workflow EAGER {
     }
 
     //
-    // SUBWORKFLOW: Sex Determine
+    // SUBWORKFLOW: Run Sex Determination
     //
 
     if ( params.run_sexdeterrmine ) {
+        ch_sexdeterrmine_input = ch_dedupped_bams
 
-    ch_sexdeterrmine_input = ch_dedupped_bams
-            .map {
-            meta, bam, bai ->
-                [ meta, bam ]
-            }
-
-    RUN_SEXDETERMINE(ch_sexdeterrmine_input, ch_sexdeterrmine_bed, ch_sexdeterrmine_samplelist)
-    ch_versions      = ch_versions.mix( RUN_SEXDETERMINE.out.versions )
-    ch_multiqc_files = ch_multiqc_files.mix( RUN_SEXDETERMINE.out.mqc.collect{it[1]}.ifEmpty([]) )
-
+        RUN_SEXDETERMINE(ch_sexdeterrmine_input, REFERENCE_INDEXING.out.sexdeterrmine_bed )
+        ch_versions      = ch_versions.mix( ESTIMATE_CONTAMINATION.out.versions )
+        ch_multiqc_files = ch_multiqc_files.mix( ESTIMATE_CONTAMINATION.out.mqc.collect{it[1]}.ifEmpty([]) )
     }
 
     //