From 9b0d58b781f4e91a7c61f0ef77760dc5df3968cc Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Tue, 13 Jun 2023 16:28:22 +0000 Subject: [PATCH] fix path --- tasks/phylogenetic_inference/task_ksnp3.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/phylogenetic_inference/task_ksnp3.wdl b/tasks/phylogenetic_inference/task_ksnp3.wdl index c74744036..6b336b4b7 100644 --- a/tasks/phylogenetic_inference/task_ksnp3.wdl +++ b/tasks/phylogenetic_inference/task_ksnp3.wdl @@ -55,7 +55,7 @@ task ksnp3 { mv -v ksnp3/core_SNPs_matrix.fasta ksnp3/~{cluster_name}_core_SNPs_matrix.fasta mv -v ksnp3/tree.core.tre ksnp3/~{cluster_name}_core.nwk - if [ -s ~{cluster_name}_core_SNPs_matrix.fasta ]; then # is the file not-empty? + if [ -s ksnp3/~{cluster_name}_core_SNPs_matrix.fasta ]; then # is the file not-empty? echo "The core SNP matrix was produced" | tee SKIP_SNP_DIST # then do NOT skip else echo "The core SNP matrix could not be produced" | tee SKIP_SNP_DIST # otherwise, skip