move comments form config to readme

conf/stjude.config

@@ -56,19 +56,7 @@ process {
     }
 
     // clusterOptions for gpu task:
-    // NOTE: gpu jobs are dispatched to HPCF's `gpu` queue
-    //
-    // To use GPU for your nextflow process:
-    // 1. GPU processes need to set the `accelerator` option in their directives. This can be configured by:
-    //   1. Adding directives in each process specifically
-    //   2. Using `process {}`-based label selectors (e.g. label 'process_gpu')
-    //
-    // 2. (optional) If you want to use docker (unsupported) or singularity (supported) on HPCF, you need to add the following container options:
-    //   containerOptions = {
-    //       workflow.containerEngine == "singularity" ? '--nv':
-    //           ( workflow.containerEngine == "docker" ? '--gpus all': null )
-    //   }
-
+    // NOTE: We use GPU exclusively in each job
     clusterOptions = { task.accelerator ? "-gpu \"num=${task.accelerator}/host:mode=shared:j_exclusive=yes\"" : null }
 }
 
@@ -79,11 +67,7 @@ singularity {
     runOptions = '-p -B "$TMPDIR"'
     pullTimeout = "3 hours"
 
-    // Directory to cache singularity images. Unavailable with an institution-level set-up.
-    // FIXME: This needs the support from the cluster administrator.
-    // Feel free to use your own directory by:
-    //   1. use `singularity.cacheDir = /path/to/your/singularity/cache` in your config.
-    //   2. set env variable: `export NXF_SINGULARITY_CACHE=/path/to/your/singularity/cache` in your shell's profile file (e.g. `~/<.bashrc/.zshrc>`).
+    // cacheDir = /path/to/your/singularity/cache
 }
 
 // clean the generated files in the working directory

docs/stjude.md

@@ -46,9 +46,14 @@ The configuration automatically selects the appropriate queue based on your task
 
 ## GPU Usage
 
+In St. Jude's HPCF cluster, the GPU jobs will be dispatched the `gpu` queue.
 To use GPUs in your pipeline:
 
-1. Set the `accelerator` option in your process directives.
+1. Set the `accelerator` option in your process directives. This can configured by:
+
+- Adding directives in each process specifically, or
+- Using `process {}`-based label selectors (e.g. label 'process_gpu')
+
 2. (Optional) If you want to use docker (unsupported) or singularity (supported) on HPCF, you need to add the following container options:
 
 ```bash
@@ -66,6 +71,14 @@ Singularity is enabled by default with the following settings:
 - Environment variables whitelist: SINGULARITY_TMPDIR, TMPDIR, CUDA_VISIBLE_DEVICES
 - Pull timeout: 3 hours
 
+### Singularity Cache Directory
+
+There is no institution-level directory setup for caching singularity images. To set the cache directory, you
+can try the following two ways:
+
+1. Add `singularity.cacheDir = /path/to/your/singularity/cache` in your nextflow config file.
+2. Set nextflow's environment variable: `export NXF_SINGULARITY_CACHE=/path/to/your/singularity/cache` in your shell's profile file (e.g. `~/<.bashrc/.zshrc>`).
+
 > [!NOTE]
 > You will need an account to use the HPC cluster at St. Jude Children's Research Hospital in order to run the pipeline. If in doubt, contact IT.