Feature/samtools sort after STAR

Sort alignment files with SAMtools instead of STAR. Fixes #182 (closed)

workflow/Snakefile

@@ -660,14 +660,23 @@ rule sort_genomic_alignment_samtools:
             "{sample}",
             "map_genome",
             "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+        prefix_temp_dir = temp(
+            directory(
+                os.path.join(
+                    config["output_dir"],
+                    "samples",
+                    "{sample}.{seqmode}",
+                    "sort_genomic_alignment_samtools")
+            )
+        )
 
     params:
         cluster_log_path = config["cluster_log_dir"],
         prefix_temp = os.path.join(
             config["output_dir"],
             "samples",
-            "{sample}",
-            "map_genome",
+            "{sample}.{seqmode}",
+            "sort_genomic_alignment_samtools",
             "temp"),
         additional_params = parse_rule_config(
             rule_config,
@@ -717,6 +726,12 @@ rule index_genomic_alignment_samtools:
             "{sample}",
             "map_genome",
             "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+        prefix_temp_dir = os.path.join(
+            config["output_dir"],
+            "samples",
+            "{sample}.{seqmode}",
+            "sort_genomic_alignment_samtools"
+        )
 
     output:
         bai = os.path.join(