Document supported environment variables

Pilot recognises some environment variables and uses them if they
are set. This adds some text to the readme so it is clear for the
user.

1 files changed, 11 insertions, 0 deletions

diff --git a/README.md b/README.md
index f9c9219..da099dc 100644
--- a/README.md
+++ b/README.md
@@ -40,6 +40,17 @@ Options can be the following:
   Use `single_machine` to run on the local node.
 * `<workflow name>` is the workflow file name without extension, e.g. `delay-calibration` or `concatenate-flag` for the VLBI pipeline or `HBA_calibrator` or `HBA_target` for LINC.
 
+## Environment variables
+
+`pilot.sh` recognises and accepts the following environment variables if set by the user:
+
+* [`APPTAINERENV_PREPEND_PATH`](https://apptainer.org/docs/user/main/environment_and_metadata.html#manipulating-path); defaults to the scripts directory of the pipeline set by `-p`.
+* [`APPTAINERENV_PYTHONPATH`](https://apptainer.org/docs/user/main/environment_and_metadata.html#apptainerenv-prefix); defaults to the scripts directory of the pipeline set by `-p`.
+* [`APPTAINER_BIND`](https://apptainer.org/docs/user/main/environment_and_metadata.html#environment-from-the-apptainer-runtime); defaults to `$HOME,$BINDDIR,$OUTPUT_DIR`, where `$OUTPUT_DIR` is set with `--outdir`.
+* `CWL_SINGULARITY_CACHE`; specifies the directory where toil can expect the software containers used by the pipeline.
+* [`TOIL_SLURM_ARGS`](https://toil.readthedocs.io/en/latest/python/toilAPIBatchsystem.html#batch-system-environment-variables); defaults to `-p cosma5 -A durham -t 72:00:00`.
+* [`TOIL_BATCH_LOGS_DIR`](https://toil.readthedocs.io/en/latest/appendices/environment_vars.html); defaults to `$OUTDIR/toil/logs`, where `$OUTDIR` is set with `--outdir`.
+
 ## Notes
 
 * Upon successful pipeline completion the results directory contains the following: