From cad3c22072d1b43554ee5beab18ee9acdf5b6561 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Apr 2024 14:44:46 +0200
Subject: [PATCH] feat: added config file to tutorial folder

---
 setup/solutions/08_Snakefile      | 22 ++++++++++++++++------
 setup/tutorial/config/config.yaml |  6 ++++++
 2 files changed, 22 insertions(+), 6 deletions(-)
 create mode 100644 setup/tutorial/config/config.yaml

diff --git a/setup/solutions/08_Snakefile b/setup/solutions/08_Snakefile
index 283e915..ca3eae6 100644
--- a/setup/solutions/08_Snakefile
+++ b/setup/solutions/08_Snakefile
@@ -1,25 +1,34 @@
-SAMPLES = ['A', 'B']
+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",
-        "data/samples/{sample}.fastq"
+        get_bwa_map_input_fastqs
     output:
-        "mapped_reads/{sample}.bam"
+        temp("mapped_reads/{sample}.bam")
+    params:
+        rg=r"@RG\tID:{sample}\tSM:{sample}"
+    log: "logs/bwa_mem/{sample}.log"
+    threads: 8
     shell:
-        "bwa mem {input} | "
-        "samtools view -Sb - > {output}"
+        "(bwa mem -R '{params.rg}' -t {threads} {input} | "
+        "samtools view -Sb - > {output}) 2> {log}"
+
 
 rule samtools_sort:
     input:
         "mapped_reads/{sample}.bam"
     output:
-        "sorted_reads/{sample}.bam"
+        temp("sorted_reads/{sample}.bam")
     shell:
         "samtools sort -T sorted_reads/{wildcards.sample} "
         "-O bam {input} > {output}"
@@ -33,6 +42,7 @@ rule samtools_index:
     shell:
         "samtools index {input}"
 
+
 rule bcftools_call:
     input:
         fa="data/genome.fa",
diff --git a/setup/tutorial/config/config.yaml b/setup/tutorial/config/config.yaml
new file mode 100644
index 0000000..fd839f5
--- /dev/null
+++ b/setup/tutorial/config/config.yaml
@@ -0,0 +1,6 @@
+samples:
+  A: A.fastq
+  B: B.fastq
+
+bwa_map:
+  rg=r"@RG\tID:{sample}\tSM:{sample}"