style: fix typos in command

CCBR · Sep 28, 2023 · 195a3d0 · 195a3d0
1 parent 4064e02
commit 195a3d0
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -225,7 +225,7 @@ 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') + " _jobby.py | tee " + join('logs', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logs', 'snakemake.log.jobby.short')
+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')
 
 onsuccess:

diff --git a/workflow/scripts/_run_jobby_on_snakemake_log b/workflow/scripts/_run_jobby_on_snakemake_log
@@ -5,10 +5,9 @@
 
 # prep the logs by pulling IDs
 snakemakelog=$1
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 jobids=$(grep --color=never "^Submitted .* with external jobid" $snakemakelog | awk '{print $NF}'  | sed "s/['.]//g" | sort | uniq | tr "\\n" " ")
 jobidswc=$(echo $jobids | wc -c)
 
 # run jobby script
 module load python
-if [ "$jobidswc" != "1" ];then ${SCRIPT_DIR}/$2 $jobids; fi
+if [ "$jobidswc" != "1" ];then python $2 $jobids; fi