1.5.6 PR (fixes #144) #145
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Made in response to /issues/144.
Currently align_trim prints a large amount of information about primer trimming to the file:
{args.sample}.alignreport.erwhich also includes raised exceptions which can lead to failures where the exception is hidden from the end user.This PR makes align_trim far less verbose by default so the stderr can be displayed during pipeline execution, any information previously stored in
{args.sample}.alignreport.eris accessible in{args.sample}.alignreport.csvin far more detail.The align_trim commands no longer pipe directly to samtools to ensure any exceptions are clearly displayed.