diff --git a/chipathlon/jobs/modules/peak_call.yaml b/chipathlon/jobs/modules/peak_call.yaml
index 2f72ca78ddbba738ffbbfb4561a7ff2656e97b15..3f68d0ab321cf4bd418abb0fec18637ff016285e 100644
--- a/chipathlon/jobs/modules/peak_call.yaml
+++ b/chipathlon/jobs/modules/peak_call.yaml
@@ -2,9 +2,9 @@ peak_call:
   - spp[tool]:
     - r_spp_nodups:
         inputs:
-          - exp.bam:
+          - exp.bed:
               type: file
-          - control.bam:
+          - control.bed:
               type: file
         additional_inputs: null
         outputs:
@@ -25,9 +25,9 @@ peak_call:
   - macs2[tool]:
     - macs2_callpeak:
         inputs:
-          - exp.bam:
+          - exp.bed:
               type: file
-          - control.bam:
+          - control.bed:
               type: file
           - prefix:
               type: argument
diff --git a/chipathlon/jobs/modules/remove_duplicates.yaml b/chipathlon/jobs/modules/remove_duplicates.yaml
index 8effc089ef445241bc93200fa3aa0b8b2a2570b1..15db58e3fc6441fb0caaf3e9e7223fb2497d3379 100644
--- a/chipathlon/jobs/modules/remove_duplicates.yaml
+++ b/chipathlon/jobs/modules/remove_duplicates.yaml
@@ -25,3 +25,11 @@ remove_duplicates:
             type: file
         - quality.qc:
             type: file
+  - bedtools_bam_to_bed:
+      inputs:
+        - no_dups.bam:
+            type: file
+      additional_inputs: null
+      outputs:
+        - no_dups.bed:
+            type: file
diff --git a/chipathlon/workflow.py b/chipathlon/workflow.py
index 4dcdc4dcc58a6af47ba053924268ffbc98d4d6e8..416a2031ac7e1bee666c5f959785f762fdd6e435 100644
--- a/chipathlon/workflow.py
+++ b/chipathlon/workflow.py
@@ -291,7 +291,7 @@ class Workflow(object):
                             job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["md5sum"])
                             self.jobs[name] = job
                             self.dax.addJob(job)
-                            # USING PEGASUS TRANSFER: 
+                            # USING PEGASUS TRANSFER:
                             # self._add_file(name, "http://" + f["url"], "dummylocal")
                             # We additionally keep track of how many input files
                             # there are to increase the number of transfer
@@ -359,8 +359,8 @@ class Workflow(object):
                 # remove_duplicates returns prefix_no_dups.bam
                 # REMEMBER: experiment is always first
                 final_prefix = run["prefix"][0] + "_" + run["prefix"][1]
-                inputs["exp.bam"] = run["prefix"][0] + "_no_dups.bam"
-                inputs["control.bam"] = run["prefix"][1] + "_no_dups.bam"
+                inputs["exp.bed"] = run["prefix"][0] + "_no_dups.bed"
+                inputs["control.bed"] = run["prefix"][1] + "_no_dups.bed"
                 if run["peak"] == "spp":
                     pass
                 elif run["peak"] == "macs2":