--- a/cfsan_centriflaken.xml	Mon Jun 27 18:19:22 2022 -0400
+++ b/cfsan_centriflaken.xml	Mon Jun 27 20:04:11 2022 -0400
@@ -7,58 +7,45 @@
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input &&
-	#for $input_dataset in $input
-	    ln -sf '$input_dataset' './cpipes-input/${input.element_identifier}';
+	#for $key in $input.keys()
+	    ln -sf '$input[$key]' './cpipes-input/$key';
 	#end for
 	pwd_path=\$(pwd) &&
 	$__tool_directory__/0.2.1/cpipes
-    #if (reads.type == "long"):
-        --pipeline centriflaken
-    #else:
-        --pipeline centriflaken_hy
+    #if ($pipeline == "centriflaken"):
+        --pipeline $pipeline
+        --fq_single_end true
+    #elif ($pipeline.name == "centriflaken_hy"):
+        --pipeline $pipeline
+        #if ($reads_lib_layout == "single"):
+            --fq_single_end true
+        #else:
+            --fq_single_end false
+        #end if
     #end if
 	--input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
-	#if ($reads.reads_lib.paired_end == "true"):
-	    --fq_single_end false
-        --fq_suffix '${reads.reads_lib.fq_suffix}'
-	    --fq2_suffix '${reads.reads_lib.fq2_suffix}'
-    #else:
-        --fq_single_end true
-        --fq_suffix '${reads.fq_suffix}'
-	#end if
+    --fq_suffix '${fq_suffix}'
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
 	--flye_genome_size '${genome_size}'
-	-profile $profile
+	-profile $runtime_profile
     ]]></command>
     <inputs>
         <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
-        <conditional name="reads">
-            <param name="type" type="select" label="Sequencing Read Library Type" value="long">
-                <option value="long">Long reads</option>
-                <option value="short">Short reads</option>
-            </param>
-            <when value="short">
-                <conditional name="reads_lib">
-                    <param name="paired_end" type="select" label="Sequencing Read Library Layout" value="false">
-                        <option value="false">Short read Single-End or Long reads</option>
-                        <option value="true">Short read Paired-End</option>
-                    </param>
-                    <when value="true">
-                        <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the FASTQ R1 file of Paired-End reads."/>
-                        <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the FASTQ R2 file of Paired-End reads."/>
-                    </when>
-                    <when value="false">
-                        <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the FASTQ R1 file of Paired-End reads."/>
-                    </when>
-                </conditional>
-            </when>
-            <when value="long">
-                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the FASTQ file of Long reads."/>
-            </when>
-        </conditional>
+        <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken"
+            help="centriflaken: for short reads (paired or unpaired). centriflaken_hy: for long reads (Nanopore or PacBio). Default: centriflaken">
+            <option value="centriflaken">centriflaken</option>
+            <option value="centriflaken_hy">centriflaken_hy</option>
+        </param>
+        <param name="read_lib_layout" type="select" label="Short Read Library Layout" value="single"
+            help="If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End">
+            <option value="single">Single-End</option>
+            <option value="paired">Paired-End</option>
+        </param>
+        <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
+        <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
         <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
             help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)"/>
         <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delimitor_idx)" />
@@ -82,11 +69,11 @@
     <tests>
         <!--Test 01: long reads-->
         <test expect_num_outputs="2">
-            <param name="input" value="FAL11127.fastq.gz" >
+            <param name="input">
                 <collection type="list">
-                    <element name="file1" value="FAL11127.fastq.gz" />
-                    <element name="file2" value="FAL11341.fastq.gz" />
-                    <element name="file3" value="FAL11342.fastq.gz" />
+                    <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
+                    <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
+                    <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
                 </collection>
             </param>
             <param name="fq_suffix" value=".fastq.gz"/>