v0.8.0

assembly_finder v0.8.0 - 24-10-2024

Simplified help output, bumped ncbi-datasets version and added option to only download summary tables.

Features

• Added option to only download summary tables by @farchaab in #24

Changes

• Updated workflows and bump tool versions by @farchaab in #23
• Simplified help output fefa389 b4b8fb6

Full Changelog: v0.7.7...v0.8.0

v0.7.7

Summary

Small release to fix docker file, update unit tests and other small fixes

Additions

• 2621c5c Added unit tests for taxa and accessions string inputs
• be970e8 Added ps in container (for usage in nextflow), and install curl, rsync and p7zip via apt

Changes

• 82c7904 Added taxon column when downloading taxa in assembly_summary.tsv
• 621e8b4 Removed curl, rsync and p7zip from env.yaml
• 066cf8a Bumped version

Fixes

• d0fc28b Return query when it does not contain GCF, GCA or "_"

PRs

• Fixed github workflows by @farchaab in #21
• Release 0.7.7 by @farchaab in #22

Full Changelog: v0.7.6...v0.7.7

Release 0.7.6

Summary

Small release to fix container, conda-envs and unit-tests

Additions

71f057b Added CITATION.cff file

Changes

• Conda:
  • 1896d62 Seperated utils conda envs
  • 6d77247 Froze env versions
  • 4175e0c Seperated csvtk and taxonkit envs
  • a8acd3c Changed conda prefix to .snakemake/conda
  • 6fce312 Use p7zip instead of unzip for extracting archive on macos
• Container:
  • 0a7e034 Added all dependencies in env.yaml

Fixes

• d845dc2 Fixed arch64 container build
• 4bbc993 Fixed XDG_CACHE_HOME
• d3cb2a9 Fixed unexpected characters in query wildcard
• 9b18f69 Include genome and seq-report by default (fixes missing input files)
• 050dff4 Fixed macos-latest unit-test

Full Changelog: v0.7.5...v0.7.6

Release 0.7.5

What's Changed

• Fix genomes paths performance by @farchaab in #16

Full Changelog: v0.7.4...v0.7.5

assembly_finder v0.7.4

Summary

Small patch to fix api-key arg

Full Changelog: v0.7.3...v0.7.4

assembly_finder v0.7.3

Summary

Small patch to download reference or representative genomes by default, and docs update

Full Changelog: v0.7.2...v0.7.3

assembly_finder v0.7.2

Summary

Small patch to fix taxonkit env and change temp directory cleanup

Full Changelog: v0.7.1...v0.7.2

Release 0.7.1

Summary

Release to add snaketool template and taxonkit for lineage taxonomy

What's Changed

• fb6d861 Added snaketool template
• 1f5f8bd Added unit tests
• c551224 Added taxonkit for lineage table
• b8f4b8d Cleanup for json and jsonl files
• 4704373 97b2b54 Added conda envs for each rule
• 8fbc583 Updated docs

Full Changelog: v0.6.2...v0.7.1

assembly_finder v0.6.2

Summary

Small release to fix version and taxonomy

What's Changed

• 6fad495 Removes floats in lineage_id, and uppercase rank
• 573e8be Adds version without empty line

Full Changelog: v0.6.1...v0.6.2

assembly_finder v0.6.1

Summary

Small release to fix spaces in genome paths

What's Changed

• edcedad Fixes spaces in genome paths
• 3583df1 Appends long metavars like lineage ranks to help

Full Changelog: v0.6.0...v0.6.1