diff --git a/src/harpy/snakefiles/sv_leviathan_pop.smk b/src/harpy/snakefiles/sv_leviathan_pop.smk
index e125f2729..f6b1d683f 100644
--- a/src/harpy/snakefiles/sv_leviathan_pop.smk
+++ b/src/harpy/snakefiles/sv_leviathan_pop.smk
@@ -110,8 +110,8 @@ rule sort_merged:
     input:
         outdir + "/workflow/input/{population}.unsort.bam"
     output:
-        bam = outdir + "/workflow/input/{population}.bam",
-        bai = outdir + "/workflow/input/{population}.bam.bai"
+        bam = temp(outdir + "/workflow/input/{population}.bam"),
+        bai = temp(outdir + "/workflow/input/{population}.bam.bai")
     log:
         outdir + "/logs/{population}.sort.log"
     resources:
diff --git a/src/harpy/snakefiles/sv_naibr_pop.smk b/src/harpy/snakefiles/sv_naibr_pop.smk
index c308b90cb..ca12d6072 100644
--- a/src/harpy/snakefiles/sv_naibr_pop.smk
+++ b/src/harpy/snakefiles/sv_naibr_pop.smk
@@ -126,8 +126,8 @@ rule sort_merged:
     input:
         outdir + "/workflow/input/{population}.unsort.bam"
     output:
-        bam = outdir + "/workflow/input/{population}.bam",
-        bai = outdir + "/workflow/input/{population}.bam.bai"
+        bam = (outdir + "/workflow/input/{population}.bam"),
+        bai = (outdir + "/workflow/input/{population}.bam.bai")
     log:
         outdir + "/logs/{population}.sort.log"
     resources:
diff --git a/src/harpy/snakefiles/sv_naibr_pop_phase.smk b/src/harpy/snakefiles/sv_naibr_pop_phase.smk
index a9c42d400..5baf8165b 100644
--- a/src/harpy/snakefiles/sv_naibr_pop_phase.smk
+++ b/src/harpy/snakefiles/sv_naibr_pop_phase.smk
@@ -253,8 +253,8 @@ rule sort_merged:
     input:
         outdir + "/workflow/input/concat/{population}.unsort.bam"
     output:
-        bam = outdir + "/workflow/input/{population}.bam",
-        bai = outdir + "/workflow/input/{population}.bam.bai"
+        bam = temp(outdir + "/workflow/input/{population}.bam"),
+        bai = temp(outdir + "/workflow/input/{population}.bam.bai")
     log:
         outdir + "/logs/{population}.sort.log"
     resources: