Implement cram chunking for PacBio and Nanopore

[reichan1998]

• Add MINIMAP2_MAPREDUCE into align_ont and align_pacbio
• Replace seqtk/subseq by bbmap/filterbyread
• Adjust resource for GENERATE_CRAM_CSV and SAMTOOLS_ADDREPLACERG

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[reichan1998]

Hi @tkchafin,
I've added some updates from patch 1.3.1 (replicated your code). Please let me know if I did anything incorrectly, and I'll make the necessary corrections.

[tkchafin]

Overall looks good and I'm able to run the full pipeline with chunking across all read types now. We can track merging the PacBio filtering into the map-reduce as a separate issue. One thing it it would be nice to track down the sources of all the WARN: The operator first is useless when applied to a value channel which returns a single value by definition warnings

[reichan1998]

Hi @tkchafin, I’ve made the changes based on your feedback. Thank you!