v6.0.0

What's Changed

• Add AMR pipeline to CLI, limit uploads to less than 500 samples, fix guided upload option for metagenomics by @valenzuelaomar in #49

• Introduces the ability to upload AMR samples (czid amr upload-samples ...etc)
• Enforces a 500 sample upload limit. When trying to upload > 500 samples, it will fail with error message: To not overwhelm CZ ID, please limit your uploads to less than 500 samples per upload, and not more than 1,000 samples per week
• Fixes guided-upload option for metagenomics
• Adds new guided-upload option for AMR

New Contributors

• @valenzuelaomar made their first contribution in #49

Full Changelog: v5.0.6...v6.0.0

v5.0.6

A bug introduced while implementing automatic lane concatenation led to the CLI no longer tuning the part size based on the total upload size. This led larger uploads to fail because their part size was too small and they exceeded the maximum number of parts. This patch fixes this bug, returning the original part size tuning behavior.

v5.0.5

What's Changed

• Make primer-bed optional for CG uploads by @lvreynoso in #46

Full Changelog: v5.0.4...v5.0.5

v5.0.4

Changelog

• 6873982 Fix file_type assignment for input_files (#44)

v5.0.3

Changelog

• f9571eb Add file_type parameter to input_files (#43)

v5.0.2

• Fixes an issue with falling back to a raw string when the location suggestion is not found that was causing this behavior to break

v5.0.1

• Fall back to the user provided string for collection locations if location suggestion is not found on the back end

v5.0.0

instead of short-read-mngs there is now a top level metagenomics command that supports bot Illumina and Nanopore as --sequencing-platform options just like consensus-genomes.

v4.1.3

Changelog

• fd10961 fix bug that breaks consensus genomes without a primer bed (#38)

v4.1.2

Changelog

• 389fa2b add better command line arg docs and checks (#37)