Update README.md with new instructions on apptainer parameter

config/slurm/README.md

@@ -35,23 +35,38 @@ conda env create -f environment.yml -p /cfs/klemming/projects/supr/sllstore.../g
 ```
 
 4) Copy the configuration file `config/slurm/profile/config_plugin_dardel.yaml` 
-to `slurm/config.yaml`. This file specifies compute resources 
-for each rule or group jobs to be run on Dardel. Any rule or 
-group job that is not listed under `set-threads` or `set-resources` 
-uses default resources specified under `default-resources`. If 
-any rule or group job fails due to too little memory or run 
-time, their compute resources can be updated in this file. Please
-add your slurm compute project ID in line 13 of `slurm/config.yaml`
-(`slurm_account`). 
-
-> Note that memory requirements are specified three times in 
-the configuration file: 1) under `set-threads` (used by Snakemake 
+to `slurm/config.yaml`. This file specifies Snakemake parameters
+that are used to run the pipeline, as well as compute resources 
+for each rule or group jobs to be run on Dardel. When you start
+the pipeline on the command line with `--profile slurm` (as
+described below), it expects a folder `slurm` with the file
+`config.yaml` therein. 
+
+The following changes to `slurm/config.yaml` are mandatory for
+the pipeline to work for you on Dardel: 
+
+- Please update the paths in line 8 (`apptainer-args`) with
+  the path to the project where all input data for GenErode
+  is located. Enter the same path before and after the `:`.
+  This is required for Apptainer (singularity) to correctly
+  bind (mount) the project directory so that the containers
+  run by the pipeline can find the input data. 
+
+- Please add your slurm compute project ID in line 13
+  (`slurm_account`). 
+
+> If any rule or group job fails due to too little memory or
+run time, their compute resources can be updated in `slurm/config.yaml`.
+Note that memory requirements are specified three times in the
+configuration file: 1) under `set-threads` (used by Snakemake 
 to specify threads in rules), 2) under `set-resources` and therein 
 under `mem_mb`, specifying the memory in Megabytes (multiplying 
 the number of threads with the available memory per thread), 
 and 3) under `set-resources` and therein under `cpus-per-task` 
 (the same number as specified under `set-threads`, required for 
-correct memory assignment on Dardel). 
+correct memory assignment on Dardel). Any rule or group job that
+is not listed under `set-threads` or `set-resources` uses the
+resources specified under`default-resources`. 
 
 5) Start GenErode the following: