feat: Salmon update

[tdayris]

Description

This PR brings an update of Salmon to 1.8

Decoys, pseudo-bams and gene-map files are handled, resources:tempdir is used to set temporary directory in salmon index. Dedicated errors are raised in salmon quant as well as deprecation warning.

Main behavior is changed in salmon index, causing a change break, since multiple input are possible now. Salmon quant interface is not changed and the update should be silent, as long as indexes are re-built by users.

You may notice the test dataset in salmon quant has changed: this is due to the new indexing method used after salmon 1.XXX. It required for unit-testing.

Also, manual decompression is not needed anymore.

QC

For all wrappers added by this PR, I made sure that

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.

[tdayris]

Hi, I solve new errors and come back here asap