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P4 stage2 init options#348

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Commits on Jul 12, 2024

• add bwa-mem2 to Dockerfile

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Commits on Jul 19, 2024

• changes to templates and ctfp to do alternate stage2 processing

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• upgrade bambi version in container to 0.18.0

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Commits on Jul 31, 2024

• allow either FASTQ or CRAM input with optional read2tags processing

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Commits on Aug 5, 2024

• always run samtools collate+reset before bambi read2tags

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Commits on Aug 13, 2024

• set defaults for samtools import flags "-i" and "-T", and make them optional

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Commits on Aug 28, 2024

• add static parameter files for stage2 reanalysis

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