made slurm jobs adapt to required threads

4fddea95 · Kevin · 4dbc3c7d · 4fddea95 · 4fddea95
Commit 4fddea95 authored Feb 04, 2019 by Kevin
Hide whitespace changes
Inline Side-by-side

Showing with 1 addition and 2 deletions

cluster.json cluster.json +0 -1

snakemake_slurm snakemake_slurm +1 -1

No files found.
--- a/cluster.json
+++ b/cluster.json
@@ -4,7 +4,6 @@
        "account" :   "MRC-BSU-SL2-GPU",
        "time" :      "06:00:00",
        "n" :          1,
-        "ncpu" :       5,
        "partition" : "bsu-gpu"
    }
 }
--- a/snakemake_slurm
+++ b/snakemake_slurm
 #!/bin/bash
 # single input: snakemake target
-nohup snakemake $1 --use-singularity -j 99 --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -n {cluster.n} -c {cluster.ncpu} -t {cluster.time}" &
+nohup snakemake $1 --use-singularity -j 99 --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -n {cluster.n} -c {threads} -t {cluster.time}" &