Update code to deal with explicit replicates and control replicates

nf-core · Jun 20, 2023 · 14e21f7 · 14e21f7
1 parent 8f1f57e
commit 14e21f7
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Showing 2 changed files with 18 additions and 7 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input       = 'https://github.com/nf-core/test-datasets/chipseq/samplesheet/v2.0/samplesheet_test.csv'
+    input       = 'https://github.com/nf-core/test-datasets/chipseq/samplesheet/v2.1/samplesheet_test.csv'
     read_length = 50
 
     // Genome references

diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
@@ -423,11 +423,19 @@ workflow CHIPSEQ {
         .set { ch_genome_bam_bai }
 
     ch_genome_bam_bai
-        .combine(ch_genome_bam_bai)
         .map {
-            meta1, bam1, bai1, meta2, bam2, bai2 ->
-                meta1.control == meta2.id ? [ meta1, [ bam1, bam2 ], [ bai1, bai2 ] ] : null
+            meta, bam, bai ->
+                meta.control ? null : [ meta.id, [ bam ] , [ bai ] ]
         }
+        .set { ch_control_bam_bai }
+
+    ch_genome_bam_bai
+        .map {
+            meta, bam, bai ->
+                meta.control ? [ meta.control, meta, [ bam ], [ bai ] ] : null
+        }
+        .combine(ch_control_bam_bai, by: 0)
+        .map { it -> [ it[1] , it[2] + it[4], it[3] + it[5] ] }
         .set { ch_ip_control_bam_bai }
 
     //
@@ -482,7 +490,10 @@ workflow CHIPSEQ {
     MACS2_CALLPEAK
         .out
         .peak
-        .filter { meta, peaks -> peaks.size() > 0 }
+        .filter {
+            meta, peaks ->
+                peaks.size() > 0
+        }
         .set { ch_macs2_peaks }
 
     // Create channels: [ meta, ip_bam, peaks ]
@@ -564,7 +575,7 @@ workflow CHIPSEQ {
     ch_deseq2_clustering_multiqc = Channel.empty()
     if (!params.skip_consensus_peaks) {
         // Create channels: [ meta , [ peaks ] ]
-            // Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
+        // Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
         ch_macs2_peaks
             .map {
                 meta, peak ->
@@ -588,7 +599,7 @@ workflow CHIPSEQ {
                     [ meta_new, peaks ]
             }
             .set { ch_antibody_peaks }
-
+        ch_antibody_peaks.dump()
         //
         // MODULE: Generate consensus peaks across samples
         //