fix: formatting

Author: cmeesters

setup_creators/tutorial/11_Snakefile_rule_params

@@ -4,66 +4,77 @@ rule all:
     input:
         "calls/all.vcf",
         "calls/positions.png",
-        "calls/quals.svg"
-        
+        "calls/quals.svg",
+
+
 def get_bwa_map_input_fastqs(wildcards):
     return config["samples"][wildcards.sample]
 
+
 rule bwa_map:
     input:
         "data/genome.fa",
-        get_bwa_map_input_fastqs
+        get_bwa_map_input_fastqs,
     output:
-        "mapped_reads/{sample}.bam"
+        "mapped_reads/{sample}.bam",
+    log:
+        "logs/bwa_map/{sample}.log",
     params:
-        rg=config["bwa_map"]["rg"]
+        rg=config['bwa_map']['rg'],
     shell:
-        "bwa mem -R '{params.rg}' {input} | samtools view -Sb - > {output}"
+        "(bwa mem -R '{params.rg}' {input} | samtools view -Sb - > {output}) 2> {log}"
 
 
 rule samtools_sort:
     input:
-        "mapped_reads/{sample}.bam"
+        "mapped_reads/{sample}.bam",
     output:
-        "sorted_reads/{sample}.bam"
+        "sorted_reads/{sample}.bam",
+    log:
+        "logs/samtools_sort/{sample}.log",
     shell:
         "samtools sort -T sorted_reads/{wildcards.sample} "
-        "-O bam -o {output} {input}"
+        "-O bam -o {output} {input} 2> {log}"
 
 
 rule samtools_index:
     input:
-        "sorted_reads/{sample}.bam"
+        "sorted_reads/{sample}.bam",
     output:
-        "sorted_reads/{sample}.bam.bai"
+        "sorted_reads/{sample}.bam.bai",
+    log:
+        "logs/samtools_index/{sample}.log",
     shell:
-        "samtools index {input}"
+        "samtools index {input} 2> {log}"
 
 
 rule bcftools_call:
     input:
         fa="data/genome.fa",
         bam=expand("sorted_reads/{sample}.bam", sample=config["samples"]),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"])
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=config["samples"]),
     output:
-        "calls/all.vcf"
+        "calls/all.vcf",
+    log:
+        "logs/bcftools_call/bcftools.log",
     shell:
-        "bcftools mpileup -f {input.fa} {input.bam} | "
-        "bcftools call -mv - > {output}"
+        "(bcftools mpileup -f {input.fa} {input.bam} | "
+        "bcftools call -mv - > {output}) 2> {log}"
+
 
 rule plot_positions:
     input:
-       rules.bcftools_call.output
+        rules.bcftools_call.output,
     output:
-       "calls/positions.png"
+        "calls/positions.png",
     script:
-       "scripts/plot-positions.py"
-       
+        "scripts/plot-positions.py"
+
+
 rule plot_quals:
     input:
-        "calls/all.vcf"
+        "calls/all.vcf",
     output:
-        "calls/quals.svg"
+        "calls/quals.svg",
     script:
         "scripts/plot-quals.py"
-