v0.1-r4

1. Install via bioconda.
2. Added an ONT Guppy2 model to the images (ont_guppy2). Click here for more benchmarking results. The results show you have to use the Guppy2 model for Guppy2 or earlier data. 3. Added google colab notebooks for quick demo. 4. Fixed a bug then there are too few variant candidates (#28).

v0.1-r3

1. Added ulimit -u (max user processes) check (lowers the THREADS if the resource is insufficient) and automatic retries on failed jobs (#20, #23, #24).
2. Added support for user-defined pileup model prefix --pileup_model_prefix and full-alignment model prefix --fa_model_prefix.
3. Added contig validity check. Contigs specified in BED but not in BAM won't be used.
4. Added an ONT Guppy5 model (ont_guppy5).

v0.1-r2

1. Fixed BED file out of range error (#12)
2. Added support for both .bam.bai and .bai BAM index filename (#10).
3. Added some boundary checks on inputs.
4. Added version checks on required packages and utilities.
5. Increased pipeline robustness.

v0.1-r1

1. Support relative path in Conda, but Docker and Singularity still require absolute path (#5).
2. Fix taskset CPU-core visibility and provide a Singularity image (#6).

v0.1

Initial release