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HumanCellAtlas / skylab

Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
BSD 3-Clause "New" or "Revised" License
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changed merged_bam output file name to sample_id.bam #352

Closed khajoue2 closed 4 years ago

khajoue2 commented 4 years ago

Purpose

Every bam made by Optimus is called merged.bam. From the DCP perspective, the infrastructure will require the outputs of pipelines to have a unique name for the entire HCA. From a user's perspective, they want certain names for their files.

Changes

changed the wdl files to take sample_id as the input and generate bam files with sample_id name instead of "merged.bam"

Review Instructions

kbergin commented 4 years ago

We discussed this in refinement - did we consider this for the implementation? Or are we thinking users will override the sample_id input with whatever they want?

We could use sample_id as default naming of pipeline outputs but give user an option to override this as an optional inputWe could use sample_id as default naming of pipeline outputs but give user an option to override this as an optional input