Feature/samtools sort after STAR

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

workflow/Snakefile

@@ -672,12 +672,6 @@ rule sort_genomic_alignment_samtools:
 
     params:
         cluster_log_path = config["cluster_log_dir"],
-        prefix_temp = os.path.join(
-            config["output_dir"],
-            "samples",
-            "{sample}.{seqmode}",
-            "sort_genomic_alignment_samtools",
-            "temp"),
         additional_params = parse_rule_config(
             rule_config,
             current_rule=current_rule,
@@ -707,7 +701,7 @@ rule sort_genomic_alignment_samtools:
     shell:
         "(samtools sort \
         -o {output.bam} \
-        -T {params.prefix_temp} \
+        -T {params.prefix_temp_dir} \
         -@ {threads} \
         {params.additional_params} \
         {input.bam}) \
@@ -726,6 +720,12 @@ 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(