Autocycler v0.5.0

The main change in v0.5.0 is that the helper scripts have now been integrated into Autocycler as a built-in subcommand:

• Instead of running canu.sh, you now run autocycler helper canu.
• This simplifies installation – no more copying Bash/Python scripts.
• The new autocycler helper command also adds features:
  • Support for Myloasm.
  • Support for different read types (e.g. PacBio HiFi).
  • Better cleanup of empty assemblies that could break pipelines.
  • Per-contig read depths where possible, with filtering options.
  • Output .log files when produced by the assembler

Other updates:

• Fixed bug with passing_clusters column in clustering.tsv file (thanks, @MrTomRod).
• Added new columns to clustering.tsv for contig header hints.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.5.0.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.5.0.tar.gz: x86-64 processors, glibc C standard library
  • I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version.
• Macs:
  • autocycler-macos-x86_64-v0.5.0.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.5.0.tar.gz: Apple silicon processors

an HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.0.tar.gz

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.