cfDNAlab 0.8.0

Main focus: This release handles the issue where running many jobs with cfdna <command> calls in parallel led to significant increased runtime due to shared-filesystem contention. It does so by introducing the --temp-dir argument for specifying a node-local scratch location for temporary files. The main contention issue was identified to be the many reads of the ref-2bit reference sequence file. By copying it into the temporary local scratch directory before processing, the issue was heavily reduced. Thanks to Anders from GenomeDK for spotting this.

• Adds --temp-dir to commands that create temporary files. This allows temporary copies of the --ref-2bit file, tile files, and other intermediate files to be placed on node-local scratch when running on HPC clusters. When omitted, temporary files remain under the output directory. cfDNAlab does not select $TMPDIR or another environment variable automatically.
• Commands that use --ref-2bit now copy the file into a unique temporary directory for each command call. This reduces shared-filesystem contention when many jobs run in parallel.
• Separates temporary processing files from temporary final-output files. Both directories remain uniquely named and are cleaned up after successful runs, errors, and Ctrl-C. Final outputs are still written to the requested output directory.