From 688b91db68487f59ab17e65c47df962bddb6c84d Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 27 Mar 2024 20:45:37 +0000 Subject: [PATCH] fixup: drop the E_indicator column https://github.com/nextstrain/dengue/pull/36#discussion_r1538211520 Since we are not using the E_indicator column, drop it. We have separate steps to calculate the E_coverage column. --- ingest/rules/nextclade.smk | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk index c99927a8..e38addc4 100644 --- a/ingest/rules/nextclade.smk +++ b/ingest/rules/nextclade.smk @@ -65,13 +65,12 @@ rule concat_nextclade_subtype_results: nextclade_field=config["nextclade"]["nextclade_field"], shell: """ - echo "{params.id_field},{params.nextclade_field},alignmentStart,alignmentEnd,genome_coverage,failedCdses,E_indicator" \ + echo "{params.id_field},{params.nextclade_field},alignmentStart,alignmentEnd,genome_coverage,failedCdses" \ | tr ',' '\t' \ > {output.nextclade_subtypes} tsv-select -H -f "seqName,clade,alignmentStart,alignmentEnd,coverage,failedCdses" {input.nextclade_results_files} \ | awk 'NR>1 {{print}}' \ - | awk -F'\t' '$2 && !($6 ~ /E/) {{print $0"\t1"; next}} {{print $0"\t"}}' \ >> {output.nextclade_subtypes} """ @@ -92,7 +91,7 @@ rule append_nextclade_columns: tsv-join -H \ --filter-file {input.nextclade_subtypes} \ --key-fields {params.id_field} \ - --append-fields {params.nextclade_field},alignmentStart,alignmentEnd,genome_coverage,failedCdses,E_indicator \ + --append-fields {params.nextclade_field},alignmentStart,alignmentEnd,genome_coverage,failedCdses \ --write-all ? \ {input.metadata} \ > {output.metadata_all}