Applied further optimisations including improvements to error messages and renaming of folders into directories.
Tested on a 50 bp single-end Illumina Run Folder.
Both steps, Illumina2bam and SortSam are now automatically skipped, if the BAM file and its corresponding MD5 sum file are present.
New BSF script to restore an Illumina Run Folder from an archive directory.
Introduced a force parameter to allow extracting over an already (partially) existing Illumina Run Folder.
Removed the --keep-old-files option from the tar command as it turns out to be version-specific.
Updated the code for the Illumina2bam BamIndexDecoder to simplify configuration files.
Improved the documentation of template files.
Applied documentation and some small code updates
Changed the Bio.BSF.Analysis.input_directory to default to the Bio.BSF.Default.directory_sequences value.
Updated the code documentation.
Updated code to convert SAM or BAM files into FASTQ files.