add time+no retries

profiles/biocloud/config.yaml

@@ -7,16 +7,18 @@ cluster:
     --qos={resources.qos}
     --cpus-per-task={threads}
     --mem={resources.mem_mb}
+    --time={resources.time}
     --job-name=smk-{rule}-{wildcards}
     --output=logs/{rule}/{rule}-{wildcards}-%j.out
 #if rules don't have resources set, use these default values.
 #Note that "mem" will be converted to "mem_mb" under the hood, so mem_mb is prefered
 default-resources:
   - partition="general"
   - qos="normal"
-  - threads=128
-  - mem_mb=1024
+  - threads=1
+  - mem_mb=512
   - gpu=0
+  - time=0-08:00:00
 #max threads per job/rule. Will take precedence over anything else. Adjust this
 #before submitting to SLURM and leave threads settings elsewhere untouched
 max-threads: 32
@@ -27,7 +29,7 @@ printshellcmds: False
 jobs: 50
 local-cores: 1
 latency-wait: 120
-restart-times: 1 #restart failed tasks this amount of times
+restart-times: 0
 max-jobs-per-second: 10 #don't touch
 keep-going: True
 rerun-incomplete: True

workflow/rules/concatenate_fastq.smk

@@ -12,7 +12,7 @@ rule concatenate_fastq:
   output:
     temp(os.path.join(config['tmp_dir'], "samples", "{sample}_concat.fastq.gz"))
   resources:
-    mem_mb = 600
+    mem_mb = 512
   threads: 1
   log:
     os.path.join(config["log_dir"], "concatenate_fastq", "{sample}.log")