Nothing too complicated for anyone familiar with WDL code, though I do worry the behavior is a bit confusing for users. There are two new parameters (only one of which is related to the title).
optical_distance which defaults to zero. If it is >0 AND mark_duplicates == true then optical dup marking will be enabled in Picard. Small-ish problem: we need to repeat ourselves because we need appropriate docs in both QC and picard.wdl. If there's a way I haven't thought of to cut down on that repetition LMK.
store_kraken_sequences is very straightforward. This should have been done a while ago but was overlooked. Tangentially related to the other changes at best, but when has this repo enforced our PRs keep a narrow scope lol.
Last change worth pointing out is that I've added the conditions under which optional outputs are created. store_kraken_sequences is related to this, because without that change this would have been bizarre.
Nothing too complicated for anyone familiar with WDL code, though I do worry the behavior is a bit confusing for users. There are two new parameters (only one of which is related to the title).
optical_distancewhich defaults to zero. If it is>0ANDmark_duplicates == truethen optical dup marking will be enabled in Picard. Small-ish problem: we need to repeat ourselves because we need appropriate docs in both QC andpicard.wdl. If there's a way I haven't thought of to cut down on that repetition LMK.store_kraken_sequencesis very straightforward. This should have been done a while ago but was overlooked. Tangentially related to the other changes at best, but when has this repo enforced our PRs keep a narrow scope lol.Last change worth pointing out is that I've added the conditions under which optional outputs are created.
store_kraken_sequencesis related to this, because without that change this would have been bizarre.