Add option to specify a separate output directory

2 files changed, 13 insertions, 10 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
diff --git a/pilot.sh b/pilot.sh
index b41f6fd..d497415 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -18,7 +18,7 @@ set_container() {
     fi
 }
 
-opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch: \
+opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch:,outdir: \
         -n 'pilot' -- "$@")
 
 eval set -- "$opts"
@@ -33,6 +33,7 @@ while true; do
         -p ) PIPELINE="${2}"; shift 2 ;;
         -r | --restart) RESTART="--restart";    shift ;;
         --scratch) SCRATCH="${2}"; shift 2 ;;
+        --outdir) OUTDIR="${2}"; shift 2;;
         * ) shift; break ;;
     esac
 done
@@ -52,14 +53,14 @@ INPUT_DIR="${2}"
 
 PIPELINE_LOG="${HOME}/${WORKFLOW_NAME}.log"
 
-TMP_OUTDIR="${INPUT_DIR}/toil/tmp/tmp/"
-JOB_LOG_DIR="${INPUT_DIR}/toil/logs/"
-BATCH_LOG_DIR="${TOIL_BATCH_LOGS_DIR:-${INPUT_DIR}/toil/logs}"
-WORK_DIR="${INPUT_DIR}/toil/work/"
-# TODO: optionally decouple output directory from input directory?
-OUTPUT_DIR="${INPUT_DIR}/${WORKFLOW_NAME}_results"
-JOBSTORE_DIR="${INPUT_DIR}/toil/${WORKFLOW_NAME}_job/"
-STATS_DIR="${OUTPUT_DIR}/stats"
+TMP_OUTDIR="${OUTDIR-$INPUT_DIR}/toil/tmp/tmp/"
+JOB_LOG_DIR="${OUTDIR-$INPUT_DIR}/toil/logs/"
+BATCH_LOG_DIR="${OUTDIR-$TOIL_BATCH_LOGS_DIR:-${INPUT_DIR}/toil/logs}"
+WORK_DIR="${OUTDIR-$INPUT_DIR}/toil/work/"
+
+OUTPUT_DIR="${OUTDIR-$INPUT_DIR}/${WORKFLOW_NAME}_results"
+JOBSTORE_DIR="${OUTDIR-$INPUT_DIR}/toil/${WORKFLOW_NAME}_job/"
+STATS_DIR="${OUTDIR-$OUTPUT_DIR}/stats"
 
 mkdir -p "$JOB_LOG_DIR"
 mkdir -p "$BATCH_LOG_DIR"