From 78ed57d61c566566036df755afacfb7795c2985f Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 27 Jan 2021 07:53:17 -0800
Subject: [PATCH] fix a few things in the Snakefile

---
 genome_grist/conf/Snakefile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/genome_grist/conf/Snakefile b/genome_grist/conf/Snakefile
index 6d98102b..bc229b54 100755
--- a/genome_grist/conf/Snakefile
+++ b/genome_grist/conf/Snakefile
@@ -39,6 +39,11 @@ def make_param_str(ksizes, scaled):
     ks = ",".join(ks)
     return f"{ks},scaled={scaled}"
 
+try:
+    os.mkdir('genbank_genomes/')
+except:
+    pass
+
 ###
 
 wildcard_constraints:
@@ -230,7 +235,7 @@ rule sourmash_reads_raw:
     input:
         r1 = outdir + "/raw/{sample}_1.fastq.gz",
         r2 = outdir + "/raw/{sample}_2.fastq.gz",
-        unp = protected(outdir + "/raw/{sample}_unpaired.fastq.gz"),
+        unp = outdir + "/raw/{sample}_unpaired.fastq.gz",
     output:
         sig = outdir + "/raw/{sample}.raw.sig"
     conda: "env/sourmash.yml"