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Fixed issue with summarize_alignments, compress_alignments and create_bar_chart tasks being re-run when resuming from successfully completed run.
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Fixed error running split_alignments_by_sample.R when an input dataset has no sampled reads, either because the input data has no reads of the sampling returns no reads due to filtering based on trimming; now uses the sample sheet to know what samples are present and creates an output file for each regardless of whether that sample was contained in the chunk.