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1357 grouping strategy applied by counting number of FASTQ files generated by FASTP #1364

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Commits on Dec 20, 2023

  1. Split FASTQs are grouped earlier for more reliable grouping strategy

    Changes:
     - The grouping strategy for sharded data has been improved
     - The number of BAM files per sample is calculated by grouping the sample by ID after splitting the FASTQ files, then counting the total number of FASTQ files created.
     - This has to wait for all FASTQ files to be produced by FASTP, but is more reliable.
     - After alignment, the number of FASTQ files is used to wait to determine the expected number of BAM files used by groupBy.
    
    Fixes #1357
    adamrtalbot committed Dec 20, 2023
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  2. Minimum number of fastqs for split_fastq is now 250

    Changes:
     - FASTP uses blocks of 250 reads when splitting a FASTQ file.
     - This update makes 250 the minimum sized block to split a FASTQ file into.
     - Updates help text accordingly
    
    Fixes #1363
    adamrtalbot committed Dec 20, 2023
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Commits on Dec 21, 2023

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  2. CHANGELOG

    adamrtalbot committed Dec 21, 2023
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  3. remove .view() statement

    adamrtalbot committed Dec 21, 2023
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