--- a/dada2_dada.xml	Mon Aug 07 01:32:01 2023 +0000
+++ b/dada2_dada.xml	Sat Dec 07 08:43:19 2024 +0000
@@ -62,14 +62,18 @@
 #if $batch_cond.batch_select == "no":
     #if len($batch_cond.derep) > 1:
     for( id in names(dada_result) ){
+        print(id)
+        print(dada_result[[id]])
         saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
     }
     #else
     #for $d in $batch_cond.derep:
+        print(dada_result)
         saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
     #end for
     #end if
 #else
+        print(dada_result)
     saveRDS(dada_result, file='$dada')
 #end if
     ]]></configfile>
@@ -116,6 +120,9 @@
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
                 <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
         <!-- default, batch -->
         <test expect_num_outputs="1">
@@ -123,6 +130,9 @@
             <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
             <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
             <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
        </test>
         <!-- test non-default options -->
         <test expect_num_outputs="1">
@@ -133,6 +143,9 @@
             <output_collection name="data_collection" type="list">
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
     </tests>
     <help><![CDATA[