GitLab

Improve targetp json structure by writing out Localization and preserving case of other fields. Also adds a script run execute targetp script quickly

Redesign databases. Introduce relative database paths. Docker steps mount the associated databases directly.

extended error handling in download_databases_from_s3bucket.sh and cleanup of logfile in main.py happens now if logfile is 1KB

databases will be downloaded without testing on availability at the first run; while downloading a lockfile is created to stop other psot instances from downloading at the same time

BUGFIX: config is now loaded while parameter functions are executed, not in the main function anymore; helper scripts are executed in the nextflow script without full path, it was made use of the bin folder in the execution directory

add download_databases function to main.py, download_databases_from_s3bucket.sh is run as subprocess

download_databases_from_s3bucket.sh tests now if folders are misssing in datadir and download only these

nextflow.config is now generated with docker and singularity scopes in which the local database directory is mounted/bind in the containers to the /databases directory; config.py now concats the right database directory with the database property in regarding modules

run scripts now print cmdline they used to run and are executed in nextflow.py as subprocesses; analysis tools are now executed in the nextflow processes directly

integrated "-l" and "-i" mode in the new nextflow workflow; nextflow config generation does not merge redudant process descriptions anymore due bugfixing

reduce_headers* and restore_headers* helper scripts now copy the input file and don't overwrite it; named scripts got an extra nextflow process and are not included in runscripts anymore; nextflow splitFasta is now at the beginning; NOTE: psot does currently not run in '-i' or '-l' mode