fix path for kraken_db specification

snake_config.yaml

@@ -28,7 +28,7 @@ SICKLE:
 ASSEMBLER:
    "minia"
 ANALYSIS:
-   "yes"
+   "no"
 
 ### Define contamination removal module
 remove_contamination:

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}"

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: