v0.10.2

Fix pypi upload

v0.10.1

• New release for Zenodo
• Increase memory for rules with retries

Full Changelog: v0.10.0...v0.10.1

v0.10.0

What's Changed

• Quality of life improvements by @AroneyS in #86
  • Rename --aviary-[gtdbtk, checkm2]-dir args to --aviary-[gtdbtk, checkm2]-db
  • Add database env variables to ibis build (SingleM, CheckM2, GTDBtk)
  • Minimise standard workflow arguments
  • Removed --no-genomes argument and made that the default
  • Set max size to 50Gbp unless single-assembly
• Add Aviary build to Ibis build by @AroneyS in #89
• Snakefile improvements by @AroneyS in #93
• Update dependencies by @AroneyS in #94
• Improve genome loading by @AroneyS in #95
• Change name to binchicken by @AroneyS in #96

Breaking changes

• Name change to binchicken
• --coassemble-output now refers to --output dir from coassemble command instead of referring to the coassemble subfolder within that output dir
• Rename --aviary-[gtdbtk, checkm2]-dir args to --aviary-[gtdbtk, checkm2]-db
• Removed --no-genomes argument and made that the default
• Set max size to 50Gbp unless single-assembly

Full Changelog: v0.9.6...v0.10.0

v0.9.6

What's Changed

• Add input to restrict coassembly samples by @AroneyS in #71
• Add SingleM metapackage env var by @AroneyS in #75
• Update Aviary env by @AroneyS in #78
• Fix using max recovery samples with single assembly by @AroneyS in #79

Full Changelog: v0.9.5...v0.9.6

v0.9.5

What's Changed

• Fix split sra downloads by @AroneyS in #59
• Prevent aviary recover output deletion by @AroneyS in #61
• Update polars to v0.19 by @AroneyS in #63
• Add more suffix options by @AroneyS in #64
• Update SingleM by @AroneyS in #65
• Skip single-ended on rerun by @AroneyS in #67
• Fix QC by @AroneyS in #68
• Update dependencies by @AroneyS in #70

Full Changelog: v0.9.4...v0.9.5

v0.9.4

What's Changed

• Switch to cores arg for snakemake by @AroneyS in #48
• Remove bbduk qc filtering by @AroneyS in #49
• Remove use of -- before target rule/file by @AroneyS in #51
• Restrict polars threads in main by @AroneyS in #53
• Switch to Fastp QC by @AroneyS in #55
• Separate read downloading by @AroneyS in #57

Full Changelog: v0.9.3...v0.9.4

v0.9.3

What's Changed

• Deduplicate contig names in incoming genomes for unmapping by @AroneyS in #40
• Add coassemble arg by @AroneyS in #42
• Filter out samples not present in forward input by @AroneyS in #45
• update kingfisher to v0.3.0 by @AroneyS in #46

Full Changelog: v0.9.2...v0.9.3

v0.9.2

What's Changed

• Better snakemake cluster support by @AroneyS in #39

Full Changelog: v0.9.1...v0.9.2

v0.9.1

What's Changed

• Fix _1 being used instead of .1 by @AroneyS in #38

Full Changelog: v0.9.0...v0.9.1

v0.9.0

What's Changed

• Fix conda env versions by @AroneyS in #21
• Switch to greedy algorithm by @AroneyS in #22
• Add build subcommand by @AroneyS in #25
• Fix target elusive memory issues by @AroneyS in #26
• Separate single-assembly from no-genomes by @AroneyS in #27
• Add new genomes input by @AroneyS in #28
• Update evaluate by @AroneyS in #29
• Improve iterate by @AroneyS in #30
• Update polars to v0.18.11 by @AroneyS in #31
• Fix cluster graph memory by @AroneyS in #32
• Fix aviary commands by @AroneyS in #33
• Update Aviary to v0.7.0 by @AroneyS in #34
• Add --new-genome-singlem argument to iterate by @AroneyS in #35
• SRA downloading improvements by @AroneyS in #36
• Support snakemake cluster by @AroneyS in #37

Full Changelog: v0.8.0...v0.9.0