style: jobby command

CCBR · Sep 29, 2023 · f326751 · f326751
1 parent 195a3d0
commit f326751
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -225,8 +225,8 @@ rule all:
 # create jobby tables
 ## command for jobby: bash scripts/_run_jobby_on_snakemake_log logs/snakemake.log _jobby.py | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short
 ## command for spooker: bash scripts/_spooker /data/sevillas2/carlisle/spook1 | tee logs/spooker.log
-jobby_cmd = join(SCRIPTSDIR, '_run_jobby_on_snakemake_log') + " " + join('logs', 'snakemake.log') + " " + join(SCRIPTSDIR, '_jobby.py') + " | tee " + join('logs', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logs', 'snakemake.log.jobby.short')
-spook_cmd = join(SCRIPTSDIR, '_spooker') + " " + WORKDIR + " | tee " + join('logs', 'spooker.log')
+jobby_cmd = "bash " + join(SCRIPTSDIR, '_run_jobby_on_snakemake_log') + " " + join('logs', 'snakemake.log') + " " + join(SCRIPTSDIR, '_jobby.py') + " | tee " + join('logs', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logs', 'snakemake.log.jobby.short')
+spook_cmd = "bash " + join(SCRIPTSDIR, '_spooker') + " " + WORKDIR + " | tee " + join('logs', 'spooker.log')
 
 onsuccess:
     print("OnSuccess")