From c57e2059e19bdbca1a6b348020291c29d1f67bc0 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 21 Feb 2020 15:50:27 +0100
Subject: [PATCH] adjust logging directory
---
Snakefile | 4 ++--
workflow/rules/paired_end.snakefile.smk | 4 ++--
workflow/rules/single_end.snakefile.smk | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index 6476351..acc07ad 100644
--- a/Snakefile
+++ b/Snakefile
@@ -353,7 +353,7 @@ rule generate_alfa_index:
singularity:
"docker://zavolab/alfa:1.1.1"
log:
- os.path.join(config["local_log"], "{organism}_{index_size}_generate_alfa_index.log")
+ os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
shell:
"alfa -a {input.gtf} \
-g {params.genome_index} \
@@ -416,7 +416,7 @@ rule alfa_bg_all_samples:
# singularity:
# "docker://zavolab/alfa:1.1.1"
conda: os.path.abspath("../../envs/env_alfa.yaml")
- log: os.path.abspath(os.path.join(config["local_log"], "ALFA", "alfa_bg_all_samples.log"))
+ log: os.path.abspath(os.path.join(config["log_dir"], "ALFA", "alfa_bg_all_samples.log"))
shell:
"""
mkdir -p {params.out_dir}; \
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 1a353fa..f61ee56 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -385,7 +385,7 @@ rule star_rpm_paired_end:
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.6.0a"
- log: os.path.join(config["local_log"], "paired_end", "{sample}", "star_rpm_paired_end.log")
+ log: os.path.join(config["log_dir"], "paired_end", "{sample}", "star_rpm_paired_end.log")
threads: 4
shell:
"""
@@ -446,7 +446,7 @@ rule alfa_bg_paired_end:
name = "{sample}"
singularity:
"docker://zavolab/alfa:1.1.1"
- log: os.path.abspath(os.path.join(config["local_log"], "paired_end", "{sample}", "alfa_bg_paired_end.log"))
+ log: os.path.abspath(os.path.join(config["log_dir"], "paired_end", "{sample}", "alfa_bg_paired_end.log"))
shell:
"""
cd {params.out_dir}; \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 8cb818f..60e539e 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -311,7 +311,7 @@ rule star_rpm_single_end:
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.6.0a"
- log: os.path.join(config["local_log"], "single_end", "{sample}", "star_rpm_single_end.log")
+ log: os.path.join(config["log_dir"], "single_end", "{sample}", "star_rpm_single_end.log")
threads: 4
shell:
"""
@@ -373,7 +373,7 @@ rule alfa_bg_single_end:
name = "{sample}"
singularity:
"docker://zavolab/alfa:1.1.1"
- log: os.path.abspath(os.path.join(config["local_log"], "single_end", "{sample}", "alfa_bg_single_end.log"))
+ log: os.path.abspath(os.path.join(config["log_dir"], "single_end", "{sample}", "alfa_bg_single_end.log"))
shell:
"""
cd {params.out_dir}; \
--
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