The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Allow
APandBXto rescue some Caenorhabditis assemblies.APrescues also assemblies in various other clades.
- Allow
NC|NZin filtered contig names, for RefSeq assemblies. - Discard contigs that match
plasmid.
- Replace
seqtk subseqwithsamtools faidxagain for performance on very large genomes. - Compress genomes with
bgzipand index them. - Add a
--assemblyscan_memoryparameter to runassembly-scanwith more memory.
- Run assemblyscan on the filtered genomes.
- Allocate only a single CPU for 1 hour with 6 Gb memory for all computations.
- Collect contig names to better check if sex chromosomes are missing from the assembly, etc.
- Replace
seqkitwith shell commands andseqtkbecause of memory usage (shenwei356/seqkit#487). This changes directory and names of output files.
- Allow TSV format and change column names to
idandfile. - Delete mitogenome files that contain more than one sequence.
- Expanded the pattern matching chromosome contigs to
^(CM|CP|FR|L[R-T]|O[U-Z]).
- Initial release of
oist/LuscombeU_stlpreprocess, created with the nf-core template.