From 507d6bfeda85a1394edb4ca16e7f0f1bf28a7286 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Fri, 10 Jan 2025 15:38:31 -0800 Subject: [PATCH] Update documentation for #178 --- docs/backend-hpc.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/backend-hpc.md b/docs/backend-hpc.md index acd5bb7..c203391 100644 --- a/docs/backend-hpc.md +++ b/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.