From bdfed737c0c5ea506727acfcd83f4815154d2f99 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Mon, 15 Mar 2021 15:48:05 +0000 Subject: [PATCH] fix typo --- tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tasks/tasks_nextstrain.wdl b/tasks/tasks_nextstrain.wdl index e190fdcd..c4c8d728 100644 --- a/tasks/tasks_nextstrain.wdl +++ b/tasks/tasks_nextstrain.wdl @@ -1452,7 +1452,7 @@ task prep_augur_metadata { echo -e "strain\tvirus\tdate\tregion\tcountry\tdivision\tlocation\tpangolin_lineage" > augur_metadata.tsv # Set strain name by assembly header - assembly_header=$(grep -e ">" ~{assembly} sed 's/>//g' ) + assembly_header=$(grep -e ">" ~{assembly} | sed 's/>//g' ) echo -e "\"$assembly_header\"\t\"ncov\"\t\"${collection_date}\"\t\"${iso_continent}\" \t\"${iso_country}\"\t\"${iso_state}\"\t\"${iso_county}\"\t"${pangolin_lineage}"" >> augur_metadata.tsv