Add option to specify a separate output directory

1 files changed, 3 insertions, 1 deletions

diff --git a/README.md b/README.md
index 883681a..88461a6 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,6 @@ This script assumes the following:
 
 * All relevant input data is available either in either the `$HOME` directory or in a directory henceforth called `$BINDDIR`.
   Targets of any links in these directories should be accessible to the compute directories, as these will be mounted during relevant jobs.
-* The output will be written to a results directory in `$BINDDIR`.
 * This script will be used with the SLURM queuing system on COSMA5 with the following options: `-p cosma5 -A durham -t 72:00:00`.
   If these options are not appropriate or if this script is to be run on other SLURM-run clusters one must set `$TOIL_SLURM_ARGS` prior to running.
 * `$CWL_SINGULARITY_CACHE` is set and the corresponding path contains (a link to) a singularity container `vlbi-cwl.sif`.
@@ -33,6 +32,9 @@ Options can be the following:
 * `--scratch` is a path to local scratch storage where temporary data can be written to (optional).
   **`--scratch` must be local to the compute node.
   Nonlocal scratch storage will likely cause the pipeline to fail.**
+* `--outdir` is a path relative to which intermediate files and final data products will be written.
+  Will be created if it does not exist.
+  If not specified, `$BINDDIR` will be used instead.
 * `<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.
 
 ## Notes