From 9e5334d83599cdef09f180c3f0411d6cf9b97e7e Mon Sep 17 00:00:00 2001 From: Matthijs van der Wild Date: Mon, 28 Oct 2024 16:13:40 +0000 Subject: Add option to specify a separate output directory --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'README.md') 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. * `` 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 -- cgit v1.2.3