From d0b0b0cedd6a0bda2f506f6d4ce363f469597a1a Mon Sep 17 00:00:00 2001
From: nikos <n.pappas@uu.nl>
Date: Tue, 8 Sep 2020 16:50:12 +0200
Subject: [PATCH] remove email address from download_genomes, fix directory
output
---
workflow/rules/construct_datasets.smk | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/workflow/rules/construct_datasets.smk b/workflow/rules/construct_datasets.smk
index a716120..37a0dbc 100644
--- a/workflow/rules/construct_datasets.smk
+++ b/workflow/rules/construct_datasets.smk
@@ -95,18 +95,16 @@ rule download_genomes:
input:
genomes_accessions = rules.process_uniprot.output.genomes_accessions
output:
- genomes_gb = "results/interaction_datasets/05_interaction_datasets/genomes.gb"
+ genomes_gb = "results/interaction_datasets/05_genomes/genomes.gb"
log:
"results/logs/construct_datasets/download_genomes.log"
- params:
- email = config.get('email')
conda:
"../envs/pvogs.yml"
shell:
"python workflow/scripts/download_genomes.py "
"-i {input.genomes_accessions} "
"-o {output.genomes_gb} "
- "-e {params.email} &>{log}"
+ "&>{log}"
rule extract_proteins_from_genomes:
input:
--
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