Update documentation for #178

docs/backend-hpc.md

@@ -13,6 +13,14 @@ Either `miniwdl` or `Cromwell` can be used to run workflows on the HPC.
 
 An [example miniwdl.cfg file](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/main/backends/hpc/miniwdl.cfg) is provided here. This should be placed at `~/.config/miniwdl.cfg` and edited to match your slurm configuration. This allows running workflows using a basic SLURM setup.
 
+> [!IMPORTANT]
+> In order to simplify workflow inputs, we make use of `map` files to specify the input data. This allows for a more concise input file, but requires changing a miniwdl configuration option to allow workflows to access files that are not expressly supplied with workflow inputs.  To enable this, add the following line to your `miniwdl.cfg` file:
+> ```ini
+> [file_io]
+> allow_any_input = true
+> ```
+> This option is already included in the example miniwdl.cfg file described in this section.
+
 ## Installing and configuring `Cromwell`
 
 Cromwell supports a number of different HPC backends; see [Cromwell's documentation](https://cromwell.readthedocs.io/en/stable/backends/HPC/) for more information on configuring each of the backends.  Cromwell can be used in a standalone "run" mode, or in "server" mode to allow for multiple users to submit workflows.  In the example below, we provide example commands for running Cromwell in "run" mode.