Add cluster support via singularity. Not yet fully tested

cluster.json

+{
+  "__default__" :
+  {
+    "n"      : "{threads}",
+    "mem"    : "500M",
+    "time"   : "10:00"
+  },
+  "mosaic_count_fixed" : 
+  {
+    "time"   : "1:00:00"
+  },
+  "mergeBams" :
+  {
+    "time"   : "1:00:00",
+	"mem"    : "2G"
+  },
+  "plot_SV_calls" :
+  {
+    "time"   : "30:00"
+  },
+  "segmentation" :
+  {
+    "time"   : "45:00",
+	"mem"    : "2G"
+  },
+
+  "mosaiClassifier_make_call" :
+  {
+    "mem"    : "2G",
+	"time"   : "45:00"
+  },
+  "plot_SV_calls" :
+  {
+    "mem"    : "2G",
+    "time"   : "25:00"
+  },
+  "run_strandphaser_per_chrom" :
+  {
+    "time"   : "1:30:00",
+    "mem"    : "6G"
+  },
+  "call_SNVs_bcftools_chrom" :
+  {
+    "time"  : "1:00:00",
+    "mem"   : "2G"
+  }
+}

run_pipeline_cluster-singularity.sh

+#!/bin/bash
+
+REF="/g/korbel/shared/datasets/refgenomes/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
+
+snakemake \
+    -j 100 \
+    --configfile Snake.config-singularity.json \
+    --use-singularity \
+	--singularity-args "-B ${REF}:/reference.fa:ro -B ${REF}.fai:/reference.fa.fai:ro" \
+	--cluster-config cluster.json \
+    --local-cores 8 \
+    --cluster "sbatch -o slurm/{rule}.%j.log -e slurm/{rule}.%j.log --cpus-per-task {cluster.n} --time {cluster.time} --mem {cluster.mem}" \
+    --latency-wait 60 \
+    --timestamp \
+    --keep-going \
+    --restart-times 1
+