From 77aeb7c4e6d1d0e5c67369658931a726d1442eac Mon Sep 17 00:00:00 2001
From: Kedi Cao <cak64153@rhskl26.uni-regensburg.de>
Date: Mon, 2 Dec 2024 17:15:13 +0100
Subject: [PATCH] fix path for kraken_db specification
---
snake_config.yaml | 2 +-
snakemodules/download_krakendb.smk | 14 +++++++-------
snakemodules/kraken.smk | 7 +------
3 files changed, 9 insertions(+), 14 deletions(-)
diff --git a/snake_config.yaml b/snake_config.yaml
index 85640c1..c07e435 100644
--- a/snake_config.yaml
+++ b/snake_config.yaml
@@ -28,7 +28,7 @@ SICKLE:
ASSEMBLER:
"minia"
ANALYSIS:
- "yes"
+ "no"
### Define contamination removal module
remove_contamination:
diff --git a/snakemodules/download_krakendb.smk b/snakemodules/download_krakendb.smk
index 1fa114f..f124019 100644
--- a/snakemodules/download_krakendb.smk
+++ b/snakemodules/download_krakendb.smk
@@ -3,14 +3,14 @@ if config["install_kraken_db"] == "yes" :
rule install_kraken_db:
output:
- directory(f"{MYPATH}/example_data/kraken_db")
+ directory(f"{kraken_db_path}")
shell:
"""
- mkdir -p {MYPATH}/example_data/kraken_db;
- wget {kraken_lib} -O {MYPATH}/example_data/kraken_db/kraken_db.tar.gz;
- tar -xzvf {MYPATH}/example_data/kraken_db/kraken_db.tar.gz -C {MYPATH}/example_data/kraken_db/;
- rm {MYPATH}/example_data/kraken_db/kraken_db.tar.gz;
+ mkdir -p {kraken_db_path};
+ wget {kraken_lib} -O {kraken_db_path}/kraken_db.tar.gz;
+ tar -xzvf {kraken_db_path}/kraken_db.tar.gz -C {kraken_db_path}/;
+ rm {kraken_db_path}/kraken_db.tar.gz;
"""
else:
- print(f"check if kraken_db already exists in {MYPATH}/example_data/kraken_db")
- kraken_db_path = f"{MYPATH}/example_data/kraken_db"
\ No newline at end of file
+ print(f"check if kraken_db already exists in {kraken_db_path}")
+ kraken_db_path = f"{kraken_db_path}"
diff --git a/snakemodules/kraken.smk b/snakemodules/kraken.smk
index a10a722..3d9efe8 100644
--- a/snakemodules/kraken.smk
+++ b/snakemodules/kraken.smk
@@ -9,7 +9,7 @@
rule kraken_map:
input:
- directory(f"{MYPATH}/example_data/kraken_db"),
+ directory(f"{kraken_db_path}"),
fq = WORK_DIR + "/{sample}/single.fastq",
p1 = WORK_DIR + "/{sample}/paired.1.fastq",
p2 = WORK_DIR + "/{sample}/paired.2.fastq"
@@ -91,11 +91,6 @@ rule index_ref:
f"{ALTREF}.bwt",
f"{ALTREF}.pac",
f"{ALTREF}.sa"
- # "example_data/chr21_remap.fa.amb",
- # "example_data/chr21_remap.fa.ann",
- # "example_data/chr21_remap.fa.bwt",
- # "example_data/chr21_remap.fa.pac",
- # "example_data/chr21_remap.fa.sa"
conda:
"envs/bwa.yml"
log:
--
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