Update igg control mapping

nf-core · Jan 31, 2024 · d4fa90d · d4fa90d
1 parent f0a800a
commit d4fa90d
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 5 deletions.
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -244,6 +244,35 @@ def check_samplesheet(file_in, file_out, use_control):
             "WARNING: Parameter --use_control was set to false, but an control group was found in " + str(file_in) + "."
         )
 
+    # Calculate the exact control/replicate id combo
+    if use_control == "true":
+        for group, reps in sorted(sample_run_dict.items()):
+
+            # Calculate the ctrl group
+            ctrl_group = None
+            is_ctrl = False
+            for replicate, info in sorted(reps.items()):
+                ctrl_group = info[0][2]
+                if ctrl_group == '':
+                    is_ctrl = True
+                break
+
+            # Continue if ctrl
+            if is_ctrl:
+                continue
+
+            # Get num reps
+            num_reps = len(reps)
+            num_ctrl_reps = len(sample_run_dict[ctrl_group])
+
+            # Assign actual ctrl rep id
+            for rep, info in sorted(reps.items()):
+                if num_reps == num_ctrl_reps:
+                    ctrl_group_new = ctrl_group + "_" + str(rep)
+                else:
+                    ctrl_group_new = ctrl_group + "_1"
+                info[0][2] = ctrl_group_new
+
     ## Write validated samplesheet with appropriate columns
     if len(sample_run_dict) > 0:
         out_dir = os.path.dirname(file_out)

diff --git a/workflows/cutandrun.nf b/workflows/cutandrun.nf
@@ -486,15 +486,14 @@ workflow CUTANDRUN {
                 /*
                 * CHANNEL: Create target/control pairings
                 */
-                ch_bedgraph_control.map{ row -> [row[0].control_group + row[0].replicate, row] }
-                .cross( ch_bedgraph_target.map{ row -> [row[0].control_group + row[0].replicate, row] } )
+                ch_bedgraph_control.map{ row -> [row[0].control_group + "_" + row[0].replicate, row] }
+                .cross( ch_bedgraph_target.map{ row -> [row[0].control_group, row] } )
                 .map {
                     row ->
                     [ row[1][1][0], row[1][1][1], row[0][1][1] ]
                 }
                 .set { ch_bedgraph_paired }
                 // EXAMPLE CHANNEL STRUCT: [[META], TARGET_BEDGRAPH, CONTROL_BEDGRAPH]
-                //ch_bedgraph_paired | view
 
                 SEACR_CALLPEAK_IGG (
                     ch_bedgraph_paired,
@@ -510,8 +509,8 @@ workflow CUTANDRUN {
                 /*
                 * CHANNEL: Create target/control pairings
                 */
-                ch_bam_control.map{ row -> [row[0].control_group + row[0].replicate, row] }
-                .cross( ch_bam_target.map{ row -> [row[0].control_group + row[0].replicate, row] } )
+                ch_bam_control.map{ row -> [row[0].control_group + "_" + row[0].replicate, row] }
+                .cross( ch_bam_target.map{ row -> [row[0].control_group, row] } )
                 .map {
                     row ->
                     [ row[1][1][0], row[1][1][1], row[0][1][1] ]