This short PR adds a utility that can convert a mix of .interval_list and .bed files into a list of just .bed files, which is ideal for pipelines using tools that only take in .bed files. The WDL is designed so that if all the inputs are .bed files, then no tasks are called (just some simple WDL code is run), and the original list and labels are returned. This means pipelines accepting just .bed files can use this task as a penalty-free (for .bed file users) way to extend their functionality to .interval_lists as well. The task also allows for optional label inputs so that labels can stay "next to" their converted file and used downstream.
See the README in this PR for more details. This utility will be used in the upcoming benchmarking WDL and others.
This short PR adds a utility that can convert a mix of
.interval_listand.bedfiles into a list of just.bedfiles, which is ideal for pipelines using tools that only take in.bedfiles. The WDL is designed so that if all the inputs are.bedfiles, then no tasks are called (just some simple WDL code is run), and the original list and labels are returned. This means pipelines accepting just.bedfiles can use this task as a penalty-free (for.bedfile users) way to extend their functionality to.interval_lists as well. The task also allows for optional label inputs so that labels can stay "next to" their converted file and used downstream.See the README in this PR for more details. This utility will be used in the upcoming benchmarking WDL and others.