diff --git a/workflows/amr/run.wdl b/workflows/amr/run.wdl
index 85e280dfa..7fe54ff0f 100644
--- a/workflows/amr/run.wdl
+++ b/workflows/amr/run.wdl
@@ -23,7 +23,7 @@ workflow amr {
         String s3_wd_uri = ""
     }
     if (defined(raw_reads_0)) {
-        Array[File]+ raw_reads = select_all([select_first([raw_reads_0]), select_first([raw_reads_1])])
+        Array[File]+ raw_reads = select_all([raw_reads_0, raw_reads_1])
 
         call host_filter.czid_host_filter as host_filter_stage { 
             input:
@@ -53,8 +53,8 @@ workflow amr {
         }
     }
 
-    Array[File]+ non_host_reads_in = select_first([RunRedup.redups_fa, select_first([non_host_reads])])
-    File contigs_in = select_first([RunSpades.contigs, select_first([contigs])])
+    Array[File]+ non_host_reads_in = select_first([RunRedup.redups_fa, select_all([non_host_reads])])
+    File contigs_in = select_first([RunSpades.contigs, select_all([contigs])])
 
     call RunRgiBwtKma {
         input: