remove spike via mapping#112
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adds a step to preprocess workflow that removes any spiked reads before running anything else. onyx percentages will now be percentages excluding spike
…_mapping_stats tuple
no longer semantically a "pass" or "fail" since reads should be removed
…en classifications
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addresses #100
Initial stab at this, so things can change if needed.
Essentially adds a mapping step to the
preprocessworkflow that runs before anything else and removes any mapped reads to be stored as a*_spikes.fastqfile (currently output to the classifications subfolder). This should also handle spike ins that contain multiple species by mapping to a concatenated reference of each in those cases. All of the unmapped reads continue through fastp, and then to the rest of Scylla.Secondly the
check_spike_statusworkflow has been changed so that it does not repeat the mapping. It still reports any detected spike ins from kraken, but the mapping stats stored inspike_count_summary.jsonnow come from the new mapping step in thepreprocessworkflow.This could be confusing as
mapped_countnow means reads removed, andclassified_countmeans any reads kraken has classified as spike after the removal process (some reads might not be removed in some scenarios I guess) - so these fields names may benefit from being changed a bit.Updated tests to reflect new bahaviour