From e20ad52afb7e01c37904a655fbbee8c24410d577 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Thu, 30 May 2024 09:44:00 +0200 Subject: [PATCH 1/2] inline root sequence --- workflow/snakemake_rules/export_for_nextstrain.smk | 1 - workflow/snakemake_rules/main_workflow.smk | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/snakemake_rules/export_for_nextstrain.smk b/workflow/snakemake_rules/export_for_nextstrain.smk index 01057da14..a7650656a 100644 --- a/workflow/snakemake_rules/export_for_nextstrain.smk +++ b/workflow/snakemake_rules/export_for_nextstrain.smk @@ -35,7 +35,6 @@ rule all_regions: input: auspice_json = expand("auspice/{prefix}_{build_name}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES), tip_frequencies_json = expand("auspice/{prefix}_{build_name}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES), - root_sequence_json = expand("auspice/{prefix}_{build_name}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES), dated_auspice_json = expand("auspice/{prefix}_{build_name}_{date}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())), dated_tip_frequencies_json = expand("auspice/{prefix}_{build_name}_{date}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())), dated_root_sequence_json = expand("auspice/{prefix}_{build_name}_{date}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())) diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk index 82922157e..ae9c532b5 100644 --- a/workflow/snakemake_rules/main_workflow.smk +++ b/workflow/snakemake_rules/main_workflow.smk @@ -1421,7 +1421,7 @@ rule export: --metadata {input.metadata} \ --node-data {input.node_data} \ --auspice-config {input.auspice_config} \ - --include-root-sequence \ + --include-root-sequence-inline \ --colors {input.colors} \ --lat-longs {input.lat_longs} \ --title {params.title:q} \ From 03a0bf39b7630cb3dd74000602b0c02ec64b0a16 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Thu, 30 May 2024 09:50:33 +0200 Subject: [PATCH 2/2] remove root sequence from expected outputs --- workflow/snakemake_rules/main_workflow.smk | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk index ae9c532b5..96b4d3886 100644 --- a/workflow/snakemake_rules/main_workflow.smk +++ b/workflow/snakemake_rules/main_workflow.smk @@ -1402,8 +1402,7 @@ rule export: lat_longs = config["files"]["lat_longs"], description = rules.build_description.output.description output: - auspice_json = "results/{build_name}/ncov_with_accessions.json", - root_sequence_json = "results/{build_name}/ncov_with_accessions_root-sequence.json" + auspice_json = "results/{build_name}/ncov_with_accessions.json" log: "logs/export_{build_name}.txt" benchmark: