| Previous changeset 48:90b09ae7e4ed (2024-12-12) Next changeset 50:16b103443761 (2024-12-12) |
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Commit message:
"planemo upload" |
|
modified:
csp2_screen.xml |
| csp2_screen.xml |
| diff -r 90b09ae7e4ed -r 6aea52d80ab9 csp2_screen.xml |
| csp2_screen.xml |
| --- 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> |