Using checkpoints for a single workflow

[danilexn]

I adapted the workflow so it only needs to call a single target rule, using checkpoints.

I have tested with the (tiny) test data and some real mouse brain samples - with and without spatial pucks, with and without puck collection, with and without meshing. Tests were run for the main, merging and downsampling workflows.

Important: I have tested all with snakemake 7.32.4. Previous versions (especially 5.x-6.x) might not work - workflow stops unexpectedly with apparently no error.

To be done before merging:

• There is an issue with the qc reports of puck_collections. When there are two run modes for a single sample, one that meshes and other that doesn't, the qc_sheet input parameters contain files from both run modes, and they have different number of columns (e.g., meshed obs do not have n_joined, and order of columns is different). I am fixing this.
• Need to see if the current tests are suitable for this (should be, the results do not change, just the number of target rules)
• Double check merging - generate pucks

[danilexn]

After merging with current master, this needs testing again