From 2ffef24a0e5d089b9befa695ce2e02013a1a2443 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Tue, 19 Mar 2024 09:00:11 -0700 Subject: [PATCH] fixup: simplify the default targets in the Snakefile --- ingest/Snakefile | 28 +--------------------------- 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/ingest/Snakefile b/ingest/Snakefile index d2b1171a..ad7e0f7c 100644 --- a/ingest/Snakefile +++ b/ingest/Snakefile @@ -8,36 +8,10 @@ configfile: "defaults/config.yaml" serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4'] -def _get_all_targets(wildcards): - # Default targets are the metadata TSV and sequences FASTA files - all_targets = expand(["results/sequences_{serotype}.fasta", "results/metadata_{serotype}.tsv"], serotype=serotypes) - - - # Add additional targets based on upload config - upload_config = config.get("upload", {}) - - for target, params in upload_config.items(): - files_to_upload = params.get("files_to_upload", {}) - - if not params.get("dst"): - print( - f"Skipping file upload for {target!r} because the destination was not defined." - ) - else: - all_targets.extend( - expand( - [f"data/upload/{target}/{{remote_file_name}}.done"], - zip, - remote_file_name=files_to_upload.keys(), - ) - ) - - return all_targets - rule all: input: - _get_all_targets, + expand(["results/sequences_{serotype}.fasta", "results/metadata_{serotype}.tsv"], serotype=serotypes) include: "rules/fetch_from_ncbi.smk"