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This pipeline tends to drop non-autosomes about halfway through (it will not thrown an error). The CWL implementation likewise handles non-autosomes oddly, but in a different way. We are working with the SBG team for more information, but for now, I gently advise against using this for non-autosomes.
I don't remember what the CWL was doing. Removing this note from the readme for now, as I fixed the dropping error and both the CWL and WDL are giving something for X, but it might be worth looking into what was going on when I wrote this.
The text was updated successfully, but these errors were encountered:
Assoc agg's readme used to say:
I don't remember what the CWL was doing. Removing this note from the readme for now, as I fixed the dropping error and both the CWL and WDL are giving something for X, but it might be worth looking into what was going on when I wrote this.
The text was updated successfully, but these errors were encountered: