fix: major rewrite of SRA download workflow

[mkatsanto]

Description

• Reimplementation of SRA download workflow with subworkflows for single and paired end samples
• Query sequencing mode (i.e., whether the library is single- or paired-ended) from SRA database (rather then setting after download based on number of generated FASTQ files)
• Add workflow test for Singularity and include in CI
• Restrict Snakemake version (<8) in zarp Conda environment to

Fixes #132
Fixes #156

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)

Conventional Commits guidelines

• I made sure the PR title follows the https://www.conventionalcommits.org/en/v1.0.0/

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• I have updated the project's documentation