Mercurial > repos > rliterman > csp2
changeset 35:106d28c851fa
"planemo upload"
| author | rliterman |
|---|---|
| date | Thu, 05 Dec 2024 16:30:58 -0500 |
| parents | 499342837ad7 |
| children | f6cd698b6f62 |
| files | csp2_snp.xml |
| diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/csp2_snp.xml Thu Dec 05 15:38:54 2024 -0500 +++ b/csp2_snp.xml Thu Dec 05 16:30:58 2024 -0500 @@ -59,7 +59,7 @@ nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy1 --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; -mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done +mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done; zip -r CSP2_Output.zip CSP2_SNP_Output; ]]> </command>