feat: 10 with log directives

setup/solutions/10_Snakefile

@@ -0,0 +1,68 @@
+configfile: "config/config.yaml"
+
+rule all:
+    input:
+        "plots/quals.svg",
+        "calls/all.vcf"
+
+
+def get_bwa_map_input_fastqs(wildcards):
+    return config["samples"][wildcards.sample]
+
+rule bwa_map:
+    input:
+        "data/genome.fa",
+        get_bwa_map_input_fastqs
+    output:
+        temp("mapped_reads/{sample}.bam")
+    params:
+        rg=config["bwa_map"]["rg"]
+    log: "logs/bwa_mem/{sample}.log"
+    threads: 8
+    shell:
+        "(bwa mem -R '{params.rg}' -t {threads} {input} | "
+        "samtools view -Sb - > {output}) 2> {log}"
+
+
+rule samtools_sort:
+    input:
+        "mapped_reads/{sample}.bam"
+    output:
+        temp("sorted_reads/{sample}.bam")
+    log: "logs/samtools_sort/{sample}.log"
+    shell:
+        "samtools sort -T sorted_reads/{wildcards.sample} "
+        "-O bam {input} > {output} 2> {log}"
+
+
+rule samtools_index:
+    input:
+         "sorted_reads/{sample}.bam"
+    output:
+         "sorted_reads/{sample}.bam.bai"
+    log: "logs/sorted_reads/{sample}.log
+    shell:
+        "samtools index {input} &> {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"])
+    output:
+        "calls/all.vcf"
+    log: "logs/bcftools.log"
+    shell:
+        "(bcftools mpileup -f {input.fa} {input.bam} | "
+        "bcftools call -mv - > {output}) &> {log}"
+
+
+rule plot_quals:
+    input:
+        "calls/all.vcf"
+    output:
+        "plots/quals.svg"
+    log: "logs/plot-quals.log"
+    script:
+        "scripts/plot-quals.py"