Adds the option to use paired-read inputs for kraken2, via the read_one and read_two arguments (or a list of two paths via inputs).

Adds/removes --paired to tool_args as necessary.

• Add Poetry, remove Twine

• Add CircleCI automatic deploy to PyPI (untested for prod PyPI)

Note: CircleCI will be failing because v0.4.0 already exists on test PyPI. That is to be expected, because I already bumped it to v0.4.0 when testing.

Adds:

• Output class returned by all toolchest.tool() calls, which contains s3_uri, presigned_s3_url, and (local) output_path variables
• S3 chaining, via supplying output.s3_uri from a previous tool as the inputs parameter for a following tool
• the ability to skip download of any tool's output, by setting output_path=None (set to None by default)

Adds:

• More STAR args
• Add multiple levels of tool_arg handling (whitelist, dangerlist, blacklist)
• Error on unknown or blacklisted args
• Reduce complexity (validation and parallelization for now) if a dangerous argument is passed

Requires:

• https://github.com/trytoolchest/toolchest-worker-node/pull/24
• https://github.com/trytoolchest/toolchest-api/pull/22

This does not fix:

• Bigger disk/memory/etc requirements for larger files where args trigger reduced complexity / no parallelization

• Adds basic whitelist options for STAR.

• Adds support for tags with variable amounts of arguments. Adds the --quantMode tag for STAR.

(This should be merged in after the kraken2 paired read commit.)

• Adds the centrifuge tool.
• Adds docs.
• Refactors how prefix_mapping is generated for megahit with a new module (input_util.py) and function (convert_input_params_to_prefix_mapping). Adds a unit test for the function.

• Refactors the tracking printed statements into a pythonic print call with string formatting.
• Fixes status update logic in uploading. (This was causing the terminal output to stall at the "uploading" stage.)
• Adds integration test dirs to .gitignore.

Pysam has caused multiple issues as a package and STAR parallelization is not currently used so this pr fully removes pysam as a dependency. Either a different library or custom sam file merging code is planned to be implemented later so parallelization framework is remaining in the code for now.

Adds basic support for running AlphaFold via Toolchest. Code needs to be cleaned up and better documented. Currently limited to 1 input fasta.

use_reduced_dbs and is_prokaryote_list are currently disabled until further implementation and testing is done. Integration will come with reduced dbs since full dbs take 45 minutes to an hour to run even on simple input.

Adds:

• Support for async execution

See https://gist.github.com/lebovic/72fbb857119f1667c7959a4d7e28cd50 (or the integration test) for a hacky example on how to run Toolchest with async execution.

Sets the version number to a default instead of erroring if the client is run from source (i.e., without the toolchest-client package being installed via pip).

Open question: the version number defaults to 0.0.0, which can be confusing -- are there any other labels that might be better (e.g., dev or just the empty string)?