Currently, our workflows assume read trimming has already occurred upstream, so we don't perform it as part of alignment. This assumption is often violated.
As part of this issue, we need to select a read trimming tool/algorithm (might require some comparative analysis) and then incorporate it into the *-core workflows. We also need to ensure there's no harm in read trimming FASTQs that have already been read trimmed.
If we opt to investigate multiple read trimming tools, we might as well write WDL tasks for all of them. It could be nice if users could select that as part of the workflow, however we may find that they are not all created equal and only one choice should be supported. TBD.
Currently, our workflows assume read trimming has already occurred upstream, so we don't perform it as part of alignment. This assumption is often violated.
As part of this issue, we need to select a read trimming tool/algorithm (might require some comparative analysis) and then incorporate it into the
*-coreworkflows. We also need to ensure there's no harm in read trimming FASTQs that have already been read trimmed.If we opt to investigate multiple read trimming tools, we might as well write WDL tasks for all of them. It could be nice if users could select that as part of the workflow, however we may find that they are not all created equal and only one choice should be supported. TBD.