Don't filter samples collected today

Closes #553
nextstrain · Feb 16, 2021 · 234fb93 · 234fb93
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commit 234fb93
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diff --git a/data/example_metadata.tsv b/data/example_metadata.tsv
@@ -1,5 +1,5 @@
 strain	virus	gisaid_epi_isl	genbank_accession	date	region	country	division	location	region_exposure	country_exposure	division_exposure	segment	length	host	age	sex	originating_lab	submitting_lab	authors	url	title	date_submitted
-Australia/VIC05/2020	ncov	?	MT450922	2020-03-05	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29812	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT450922	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC05/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11
+Australia/VIC05/2020	ncov	?	MT450922	2021-02-16	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29812	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT450922	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC05/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11
 Australia/VIC1000/2020	ncov	?	MT451684	2020-03-31	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29806	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT451684	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1000/2020, complete genome	2020-05-11
 Australia/VIC1008/2020	ncov	?	MT451690	2020-03-31	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29806	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT451690	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1008/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11
 Australia/VIC1018/2020	ncov	?	MT451699	2020-04-01	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29813	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT451699	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1018/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11

diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
@@ -260,7 +260,7 @@ rule filter:
         exclude_where = config["filter"]["exclude_where"],
         min_date = config["filter"]["min_date"],
         ambiguous = lambda wildcards: f"--exclude-ambiguous-dates-by {config['filter']['exclude_ambiguous_dates_by']}" if "exclude_ambiguous_dates_by" in config["filter"] else "",
-        date = date.today().strftime("%Y-%m-%d")
+        date = (date.today() + datetime.timedelta(days=1)).strftime("%Y-%m-%d")
     conda: config["conda_environment"]
     shell:
         """