fix: biowulf has depreceated SLURM_JOBID in favor of SLURM_JOB_ID

CCBR · May 23, 2024 · 3d6470c · 3d6470c
1 parent e828a99
commit 3d6470c
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@
 - Change the peak widths histogram type from overlay to stack. (#176, @kelly-sovacool)
 - Add a workflow entry point to download fastq files from SRA. (#176, @kelly-sovacool)
 - Add `test_human` profile with chipseq data from ENCODE. (#176, @kelly-sovacool)
+- In biowulf config profile, switch variable $SLURM_JOBID to $SLURM_JOB_ID. (@kelly-sovacool)
 
 ## CHAMPAGNE 0.3.0
 

diff --git a/conf/biowulf.config b/conf/biowulf.config
@@ -27,7 +27,7 @@ singularity {
 env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS"
 
 process.clusterOptions = ' --gres=lscratch:200 '
-process.scratch = '/lscratch/$SLURM_JOBID'
+process.scratch = '/lscratch/$SLURM_JOB_ID'
 process.stageInMode = 'symlink'
 process.stageOutMode = 'rsync'
 // for running pipeline on group sharing data directory, this can avoid inconsistent files timestamps