# HG changeset patch
# User rliterman
# Date 1733259392 18000
# Node ID 5c609acba34e1330a4392d01c13b590208477fcc
# Parent  75070dbe67b11821624b64e4934fa7b578caf658
"planemo upload"

diff -r 75070dbe67b1 -r 5c609acba34e CSP2/subworkflows/fetchData/main.nf
--- a/CSP2/subworkflows/fetchData/main.nf	Tue Dec 03 15:15:27 2024 -0500
+++ b/CSP2/subworkflows/fetchData/main.nf	Tue Dec 03 15:56:32 2024 -0500
@@ -21,6 +21,8 @@
 
 // Set SKESA cores to 4 or fewer
 skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
+println "params.cores: ${params.cores}"
+println "skesa_cpus: ${skesa_cpus}"
 
 workflow {
     main:
diff -r 75070dbe67b1 -r 5c609acba34e csp_screen.xml
--- a/csp_screen.xml	Tue Dec 03 15:15:27 2024 -0500
+++ b/csp_screen.xml	Tue Dec 03 15:56:32 2024 -0500
@@ -60,6 +60,7 @@
 		nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
 
 		zip -r work.zip work
+		zip -r csp2.zip CSP2_Screen_Output
 	]]>
 	</command>
 	<inputs>
@@ -85,6 +86,7 @@
 		<data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
 		<data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
 		<data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
+                <data name="out_dir" format="zip" label="CSP2 Directory" from_work_dir="csp2.zip" />
                 <data name="work_dir" format="zip" label="Nextflow Work Directory" from_work_dir="work.zip" />
 	</outputs>
 	<tests>