Mercurial > repos > rliterman > csp2

diff csp2_screen.xml @ 49:6aea52d80ab9

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 16:06:13 -0500
parents 90b09ae7e4ed
children 16b103443761
line wrap: on
line diff
--- a/csp2_screen.xml	Thu Dec 12 15:52:59 2024 -0500
+++ b/csp2_screen.xml	Thu Dec 12 16:06:13 2024 -0500
@@ -57,7 +57,10 @@
         export REF_ID_ARG="";
 fi;
 
-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 --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
+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 --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
+ls -la CSP2_Screen_Output &&
+sleep 5 &&
+ls -la CSP2_Screen_Output &&
 cp CSP2_Screen_Output/Screening_Results.tsv CSP2_Screen_Output/Raw_MUMmer_Summary.tsv CSP2_Screen_Output/Isolate_Data.tsv output/;
 ]]>
         </command>