...

config/cluster.json

-{
-    "__default__" :
-    {
-        "account"       : "MRC-BSU-SL2-CPU",
-        "partition"     : "skylake",
-        "time"          : "02:00:00",
-        "ntasks"        : "1",
-        "nodes"         : "1",
-        "ncpu"          : "1",
-        "name"          : "{rule}__{wildcards}",
-        "output"        : "logs/{rule}__{wildcards}.out",
-        "error"         : "logs/{rule}__{wildcards}.out"
-    }
-}

config/snakemake/default/config.yaml

+use-singularity:    True
+singularity-args:   "-H $PWD"
+singularity-prefix: "."

config/snakemake/mrc-bsu-cluster/config.yaml

+jobs:               20
+use-singularity:    True
+cluster:            "sbatch -A MRC-BSU-SL2-CPU -p skylake --ntasks 1 --cpus-per-task 1 --nodes 1 -t 02:00:00 --job-name '{rule}__{wildcards}' --output '{rule}__{wildcards}.out' --error '{rule}__{wildcards}.err'"
+singularity-args:   "-H $PWD"
+singularity-prefix: "."

scripts/singularity.def

@@ -26,7 +26,7 @@ From: rocker/verse:3.6.2
     # install bcftools
     export BCFVER=1.10.2
     apt-get -y install \
-        gcc wget make zlib1g zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev
+        gcc wget make zlib1g zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev pv
     wget https://github.com/samtools/bcftools/releases/download/$BCFVER/bcftools-$BCFVER.tar.bz2
     tar -xvjf bcftools-$BCFVER.tar.bz2
     cd bcftools-$BCFVER