fix: set default tmp dir for biowulf & frce

kelly-sovacool commented 10 months ago

Changes

Automatically set it to lscratch/$SLURM_JOBID on biowulf or the OUTPUT argument on FRCE. Still allow users to override the default by setting --tmp-dir on the CLI.

Issues

Fixes #79

Testing

[x] biowulf
[x] frce

without tmp-dir flag on either platform

#!/usr/bin/env bash
RENEE_DIR=/mnt/projects/CCBR-Pipelines/pipelines/RENEE/renee-dev-sovacool
WORKDIR=/scratch/cluster_scratch/$USER/renee_test_v2.5.11
rm -rf $WORKDIR

module load singularity
$RENEE_DIR/bin/renee run \
    --input $RENEE_DIR/.tests/*.R?.fastq.gz \
    --output $WORKDIR \
    --genome hg38_30 \
    --mode slurm \
    --sif-cache /mnt/projects/CCBR-Pipelines/SIFs

PR Checklist

(~Strikethrough~ any points that are not applicable.)

[x] This comment contains a description of changes with justifications, with any relevant issues linked.
[x] Update docs if there are any API changes.
[x] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

slsevilla commented 10 months ago

There's a typo in your description changes - can you add the default for force? (right now it says 'out', above)

kelly-sovacool commented 10 months ago

This works for me now on both biowulf and frce, just waiting on @slsevilla's test to complete successfully too.

CCBR / RENEE