Add resource specifications to all Snakemake rules

[Copilot]

All Snakemake rules now specify threads, mem_mb, and runtime (in minutes) as integers for proper cluster resource allocation.

Changes

workflow/rules/import.smk - 8 rules updated

• Simple I/O tasks (extract_sample, copy_blaze_metadata): threads=1, mem_mb=1000-4000, runtime=10-60
• Metadata extraction (blaze_to_metadata*, prestitched_to_metadata): threads=1, mem_mb=2000, runtime=60
• Data conversion (tif_to_zarr_gcs, bioformats_to_zarr, concat_tiles): runtime=240-360 added

workflow/rules/imaris.smk - 1 rule updated

• imaris_to_metadata: threads=1, mem_mb=2000, runtime=60

workflow/rules/ome_zarr.smk - 2 rules updated

• zarr_to_ome_zarr: runtime=480
• ome_zarr_to_nii: mem_mb=16000, runtime=120

workflow/rules/qc.smk - 6 rules updated

• QC generation tasks: threads=1, mem_mb=1000-8000, runtime=10-60

workflow/rules/multiview_stitcher.smk - 3 rules updated

• Registration/fusion: runtime=240-480
• Plotting: threads=1, mem_mb=4000, runtime=30

Example

rule extract_sample:
    threads: 1
    resources:
        mem_mb=4000,
        runtime=60,  # minutes

Original prompt

Ensure all rules have threads set, and for resources: mem_mb, and runtime . All are ints, runtime in minutes. If unsure set runtime to 60

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