- use of...

- use of [`temp()`](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=temp#protected-and-temporary-files) 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`](https://snakemake.readthedocs.io/en/stable/executing/cli.html?highlight=notemp#BEHAVIOR) 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`](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=shadow#shadow-rules) 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 for setting an optional `shadow prefix`, especially useful in cluster execution
- See comment in #137 for impact of disk space savings on a real-world dataset
- correctly add snakemake `{threads}` in execution in rules
  - fastqc
  - quantification_kallisto

Fixes #137.