From fa45c8fd4609b92a98643370f35aa11b32d0b890 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Mon, 9 Sep 2019 17:23:48 +0200
Subject: [PATCH] catalogue debug
---
annotation.smk | 2 +-
catalogue.smk | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/annotation.smk b/annotation.smk
index 016375d..d781d61 100644
--- a/annotation.smk
+++ b/annotation.smk
@@ -41,7 +41,7 @@ rule prodigal:
def faa_input(wildcards):
if wildcards.sample == "catalogue":
- return ["work/cdhit/catalogue.faa"]
+ return {"faa": "work/cdhit/catalogue.faa"}
else :
if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
return {"faa": "work/FGS/{wildcards.sample}/{wildcards.sample}_FGS.faa".format(wildcards=wildcards)}
diff --git a/catalogue.smk b/catalogue.smk
index 55eae87..a0db98c 100644
--- a/catalogue.smk
+++ b/catalogue.smk
@@ -83,10 +83,10 @@ rule cd_hit_2D:
rule faa_catalogue:
input:
- ffn = "work/cdhit/catalogue.ffn"
- faa = expand("work/prodigal/{sample}/{sample}.faa", sample=config["SAMPLES"])
+ ffn = "work/cdhit/catalogue.ffn",
+ faa = expand("work/prodigal/{sample}/{sample}_prodigal.faa", sample=config["SAMPLES"])
output:
- list = temp("work/cdhit/catalogue.list")
+ list = temp("work/cdhit/catalogue.list"),
faa = "work/cdhit/catalogue.faa"
threads:
2
--
GitLab