Feature/samtools sort after STAR

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

workflow/Snakefile

@@ -665,7 +665,7 @@ rule sort_genomic_alignment_samtools:
                 os.path.join(
                     config["output_dir"],
                     "samples",
-                    "{sample}",
+                    "{sample}.{seqmode}",
                     "sort_genomic_alignment_samtools")
             )
         )
@@ -675,7 +675,7 @@ rule sort_genomic_alignment_samtools:
         prefix_temp = os.path.join(
             config["output_dir"],
             "samples",
-            "{sample}",
+            "{sample}.{seqmode}",
             "sort_genomic_alignment_samtools",
             "temp"),
         additional_params = parse_rule_config(
@@ -726,6 +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(