--- a/csp2_snp.xml	Thu Dec 12 18:30:42 2024 -0500
+++ b/csp2_snp.xml	Fri Dec 13 08:49:33 2024 -0500
@@ -6,41 +6,40 @@
         </requirements>
         <version_command>nextflow -version</version_command>
         <command detect_errors="aggressive"><![CDATA[
-export CSP2_DIR=\$PWD;
-mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references;
+mkdir ./queries ./references;
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
         #for query in $query_fasta:
-                        ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier};
+                        ln -sf ${query} ./queries/${query.element_identifier};
         #end for
-        export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries";
+        export QUERY_FASTA_ARG="--fasta ./queries";
 else
         export QUERY_FASTA_ARG="";
 fi;
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
         #for query in $query_reads:
-                ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier};
+                ln -sf ${query} ./queries/${query.element_identifier};
         #end for
-        export QUERY_READS_ARG="--reads \$CSP2_DIR/queries";
+        export QUERY_READS_ARG="--reads ./queries";
 else
         export QUERY_READS_ARG="";
 fi;
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
         #for ref in $ref_fasta:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier};
+                ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references";
+        export REF_FASTA_ARG="--ref_fasta ./references";
 else
         export REF_FASTA_ARG="";
 fi;
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
         #for ref in $ref_reads:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier};
+                ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_READS_ARG="--ref_reads \$CSP2_DIR/references";
+        export REF_READS_ARG="--ref_reads ./references";
 else
         export REF_READS_ARG="";
 fi;
@@ -57,9 +56,12 @@
         export RESCUE_ARG="";
 fi;
 
-nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
+nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 &&
+ls -la CSP2_SNP_Output/SNP_Analysis/* &&
+mkdir CSP2_Output &&
+cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv';  cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done &&
+ls -la CSP2_Output;
 
-zip -r CSP2_Output.zip CSP2_SNP_Output;
 ]]>
         </command>
         <inputs>
@@ -82,16 +84,23 @@
                 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
         </inputs>
         <outputs>
-                <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
                 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
                 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
-                <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
-                <collection name="reference_results" type="list:list">
-                        <discover_datasets pattern="*/CSP2_SNP_Pipeline.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
-                        <discover_datasets pattern="*/Reference_Screening.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
-                        <discover_datasets pattern="*/snp_distance_matrix_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
-                        <discover_datasets pattern="*/snp_distance_pairwise_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
-                        <discover_datasets pattern="*/snpma_preserved.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                
+                <collection name="csp2_logs" type='list' label="CSP2 Log">
+                        <discover_datasets pattern="(?P&lt;designation&gt;.+)_CSP2_SNP_Pipeline\.log" directory="CSP2_Output" format='txt'/>
+                </collection>
+                <collection name="csp2_alignments" type='list' label="CSP2 Alignment">
+                        <discover_datasets pattern="(?P&lt;designation&gt;.+)_snpma_preserved\.fasta" directory="CSP2_Output" format='fasta'/>
+                </collection>
+                <collection name="csp2_matrices" type='list' label="CSP2 Matrices">
+                        <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_matrix_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
+                </collection>
+                <collection name="csp2_pairwise" type='list' label="CSP2 Pairwise Distances">
+                        <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_pairwise_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
+                </collection>
+                <collection name="csp2_ref_screening" type='list' label="CSP2 Reference Screening">
+                        <discover_datasets pattern="(?P&lt;designation&gt;.+)_Reference_Screening\.tsv" directory="CSP2_Output" format='tabular'/>
                 </collection>
         </outputs>
         <tests>