WIP: update genome-grist to modern days (May 2025)

[ctb]

tackling #312

current status: make works :)

• move Snakefile to main dir
• move env under main dir
• investigate: parallelism with -c not working!?
• investigate: add benchmark foo? singlesketch, gather, others?
• upgrade summarize with weighted!
• consider: switch to prefetch per https://github.com/ncbi/workshop-asm-ngs-2024/wiki/3.3-Using-SRAToolkit-to-retrieve-Data
• fix pytest tests
• adjust config file(s) for removed flags / issue warnings
• detect non-paired-end??

[ctb]

Current runtime for conf-paper.yml, starting from FASTQ files:

        Command being timed: "genome-grist run conf-paper.yml summarize_sample_info -c 64"
        User time (seconds): 20809.18
        System time (seconds): 329.86
        Percent of CPU this job got: 473%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 1:14:22
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 25465616
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 559048
        Minor (reclaiming a frame) page faults: 17469163
        Voluntary context switches: 822568
        Involuntary context switches: 1938318
        Swaps: 0
        File system inputs: 183824800
        File system outputs: 2896016
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

[ctb]

whew! merging and releasing.