From fbc972a926ff4654d04f56e950d1b101d2542535 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 21 Feb 2024 13:44:58 -0800 Subject: [PATCH] Update docs of nextclade.smk --- ingest/workflow/snakemake_rules/nextclade.smk | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk index a2e848f1..6f5b7fa4 100644 --- a/ingest/workflow/snakemake_rules/nextclade.smk +++ b/ingest/workflow/snakemake_rules/nextclade.smk @@ -1,3 +1,24 @@ +""" +This part of the workflow handles running Nextclade on the curated metadata +and sequences. + +REQUIRED INPUTS: + + metadata = data/metadata_all.tsv + sequences = results/sequences_{serotype}.fasta + nextclade_datasets = ../nextclade_data/{serotype} + +OUTPUTS: + + metadata = results/metadata_{serotype}.tsv + sequences = results/sequences_{serotype}.fasta + nextclade = results/nextclade_subtypes.tsv + +See Nextclade docs for more details on usage, inputs, and outputs if you would +like to customize the rules: +https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html +""" + SUPPORTED_NEXTCLADE_SEROTYPES = ['denv1', 'denv2', 'denv3', 'denv4'] SEROTYPE_CONSTRAINTS = '|'.join(SUPPORTED_NEXTCLADE_SEROTYPES)