From c932c002bcacac4a485eb902d654f80c19f44ef8 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Tue, 28 Mar 2023 11:15:41 -0700 Subject: [PATCH] fix: makes the compress rule more generic Co-authored-by: Thomas Sibley --- ingest/workflow/snakemake_rules/transform.smk | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk index 6fb36cc7..72df12c6 100644 --- a/ingest/workflow/snakemake_rules/transform.smk +++ b/ingest/workflow/snakemake_rules/transform.smk @@ -107,25 +107,24 @@ rule transform: --sequence-field {params.sequence_field} ) 2>> {log} """ + rule post_process_metadata: input: metadata="data/raw_metadata_{serotype}.tsv", output: metadata="data/metadata_{serotype}.tsv", shell: - """ + """ ./bin/post_process_metadata.py --metadata {input.metadata} --outfile {output.metadata} """ + rule compress: input: - sequences="data/sequences_{serotype}.fasta", - metadata="data/metadata_{serotype}.tsv", + file="{a_file}", output: - sequences="data/sequences_{serotype}.fasta.zst", - metadata="data/metadata_{serotype}.tsv.zst", + file_compressed="{a_file}.zst", shell: """ - zstd -T0 -o {output.sequences} {input.sequences} - zstd -T0 -o {output.metadata} {input.metadata} - """ \ No newline at end of file + zstd -T0 -o {output.file_compressed} {input.file} + """