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).
Edited by Dominik Burri