From 2f9abe829689914a07fd874eb40d2bad102c8f10 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Wed, 31 Mar 2021 16:43:10 +0000 Subject: [PATCH] use pangolin_lineage as tsv header --- tasks/tasks_nextstrain.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tasks/tasks_nextstrain.wdl b/tasks/tasks_nextstrain.wdl index 6338da93..86f2069f 100644 --- a/tasks/tasks_nextstrain.wdl +++ b/tasks/tasks_nextstrain.wdl @@ -126,7 +126,7 @@ task derived_cols { String? lab_highlight_loc Array[File] table_map=[] - String docker="quay.io/broadinstitute/viral-core:2.1.19-rc2" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { lab_highlight_loc: { @@ -541,7 +541,7 @@ task filter_sequences_by_length { File sequences_fasta Int min_non_N = 1 - String docker="quay.io/broadinstitute/viral-core:2.1.19-rc2" + String docker="quay.io/broadinstitute/viral-core:2.1.19" } parameter_meta { sequences_fasta: { @@ -1449,7 +1449,7 @@ task prep_augur_metadata { # de-identified consensus/assembly sequence year=$(echo ${collection_date} | cut -f 1 -d '-') - echo -e "strain\tvirus\tdate\tregion\tcountry\tdivision\tlocation\tpango_lineage" > augur_metadata.tsv + echo -e "strain\tvirus\tdate\tregion\tcountry\tdivision\tlocation\tpangolin_lineage" > augur_metadata.tsv # Set strain name by assembly header assembly_header=$(grep -e ">" ~{assembly} | sed 's/\s.*$//' | sed 's/>//g' )