snakemake deploy adaptions

workflow/Snakefile

@@ -6,7 +6,7 @@ from pathlib import Path
 configfile: "config/config.yaml"
 
 
-#sample_file = Path.joinpath(Path(".."), Path(config["sample_file"]))
+# sample_file = Path.joinpath(Path(".."), Path(config["sample_file"]))
 sample_file = Path(config["sample_file"])
 samples = read_table(sample_file)["sample_name"].tolist()
 

workflow/rules/align.smk

@@ -1,10 +1,10 @@
 # mapping of the reads to the reference genome using Burrows-Wheeler Aligner
 rule bwa_mem:
     input:
-        amb="{{reference_path}}/{reference}.fa.amb",
-        ref="{{reference_path}}/{reference}.fa",
-        fastq_r1="{{data_path}}/{sample}_R1.fastq.gz",
-        fastq_r2="{{data_path}}/{sample}_R2.fastq.gz",
+        amb = Path.joinpath(Path(config["reference_path"]), "{reference}.fa.amb"),
+        ref = Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
+        fastq_r1=Path.joinpath(Path(config["data_path"]), "{sample}_R1.fastq.gz"),
+        fastq_r2=Path.joinpath(Path(config["data_path"]), "{sample}_R2.fastq.gz"),
     wildcard_constraints:
         reference="[A-Za-z0-9]+",
     output:
@@ -36,12 +36,12 @@ rule idx_bam:
 # creates index for the reference sequence in fasta format
 rule idx_fasta:
     input:
-        "{{reference_path}}/{reference}.fa",
+         Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
     output:
-        "{{reference_path}}/{reference}.fa.fai",
+         Path.joinpath(Path(config["reference_path"]), "{reference}.fa.fai"),
     conda:
         "../envs/samtools.yaml"
-    log:
-        "logs/{{reference_path}}/{reference}/idx_fasta.log",
+    #log:
+    #    "logs/{{reference_path}}/{reference}/idx_fasta.log",
     shell:
         "samtools faidx {input}"

workflow/rules/consensus_sequence.smk

@@ -18,7 +18,7 @@ rule prepare_for_seq:
 # creates the consensus sequence
 rule vcf_to_fasta:
     input:
-        ref="{{reference_path}}/{reference}.fa",
+        ref=Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
         vcf="results/sequences/{caller}/{reference}/{sample}.vcf.gz",
         index="results/sequences/{caller}/{reference}/{sample}.vcf.gz.tbi",
     output:

workflow/rules/reference.smk

@@ -1,9 +1,9 @@
 # downloading the mitochondrial reference genome for mouse, dog and human data
 rule get_ref:
     output:
-        "{{reference_path}}/{reference}.fa",
-    log:
-        "logs/{{reference_path}}/{reference}/get_ref.log",
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
+    #log:
+    #    "logs/{{reference_path}}/{reference}/get_ref.log",
     run:
         if config["reference"] == "mouse":
             shell(
@@ -22,18 +22,18 @@ rule get_ref:
 # creates the index for the reference genome
 rule bwa_idx:
     input:
-        "{{reference_path}}/{reference}.fa",
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
     output:
-        "{{reference_path}}/{reference}.fa.amb",
-        "{{reference_path}}/{reference}.fa.ann",
-        "{{reference_path}}/{reference}.fa.bwt",
-        "{{reference_path}}/{reference}.fa.pac",
-        "{{reference_path}}/{reference}.fa.sa",
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa.amb"),
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa.ann"),
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa.bwt"),
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa.pac"),
+        Path.joinpath(Path(config["reference_path"]), "{reference}.fa.sa"),
     wildcard_constraints:
         reference="[A-Za-z0-9]+",
     conda:
         "../envs/bwa.yaml"
-    log:
-        "logs/{{reference_path}}/{reference}/bwa_idx.log",
+    #log:
+    #    "logs/{{reference_path}}/{reference}/bwa_idx.log",
     shell:
         "bwa index {input}"

workflow/rules/variants_bcftools.smk

@@ -6,8 +6,8 @@ rule call_variants:
     input:
         bam="results/mapped/{reference}/{sample}.bam",
         bamidx="results/mapped/{reference}/{sample}.bam.bai",
-        ref="{{reference_path}}/{reference}.fa",
-        index="{{reference_path}}/{reference}.fa.fai",
+        ref = Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
+        index = Path.joinpath(Path(config["reference_path"]), "{reference}.fa.fai"),
     output:
         "results/calls_bcftools/{reference}/{sample}.vcf",
     wildcard_constraints:
@@ -24,7 +24,7 @@ rule call_variants:
 rule normalize_variants:
     input:
         vcf="results/calls_bcftools/{reference}/{sample}.vcf.gz",
-        ref="{{reference_path}}/{reference}.fa",
+        ref = Path.joinpath(Path(config["reference_path"]), "{reference}.fa"),
     output:
         "results/calls_bcftools/{reference}/norm_{sample}.vcf",
     conda: