Remove unnecessary files in results directory

• use of temp() statements in snakemake rules
  • extract_transcriptome
  • concatenate_transcriptome_and_genome
  • extract_transcripts_as_bed12
  • calculate_TIN_scores
  • star_rpm
  • rename_star_rpm_for_alfa
  • alfa_qc
  • sort_bed_4_big
  • pe_remove_adapters_cutadapt
  • pe_remove_polya_cutadapt
  • remove_adapters_cutadapt
  • remove_polya_cutadapt
• use of --notemp in test scripts (local and slurm) for successful execution without removing temp files
  • test_alfa
  • test_create_dag_image
  • test_create_rule_graph
  • test_integration_worklow
  • test_integration_workflow_multiple_lanes
• use of shadow directive in rules
  • star_rpm
  • pe_map_genome_star
  • pe_quantification_salmon
  • pe_genome_quantification_kallisto
  • map_genome_star
  • quantification_salmon
  • genome_quantification_kallisto
• See comment in #137 (closed) for setting an optional shadow prefix, especially useful in cluster execution
• See comment in #137 (closed) for impact of disk space savings on a real-world dataset
• correctly add snakemake {threads} in execution in rules
  • fastqc
  • quantification_kallisto

Closes #137 (closed).

Snakefile

@@ -38,12 +38,6 @@ if cluster_config:
 include: os.path.join("workflow", "rules", "paired_end.snakefile.smk")
 include: os.path.join("workflow", "rules", "single_end.snakefile.smk")
 
-onsuccess:
-    print("Workflow finished, no error.")
-    os.system("rm -rv " + config['kallisto_indexes'])
-    os.system("rm -rv " + config['salmon_indexes'])
-    os.system("rm -rv " + config['alfa_indexes'])
-
 rule finish:
     """
         Rule for collecting outputs