diff --git a/config/.singularity.config.swp b/config/.singularity.config.swp
deleted file mode 100644
index ad1069b..0000000
Binary files a/config/.singularity.config.swp and /dev/null differ
diff --git a/config/test_pbs.config b/config/test_pbs.config
deleted file mode 100644
index eb5ff49..0000000
--- a/config/test_pbs.config
+++ /dev/null
@@ -1,180 +0,0 @@
-singularity {
-    /* Enables Singularity container execution by default */
-    enabled = true
-    cacheDir = "$PWD"
-    /* Enable auto-mounting of host paths (requires user bind control feature enabled */
-    autoMounts = true
-}
-
-env {
-    /* Location of trimmomatic jar file */
-    TRIMMOMATIC = '/opt/Trimmomatic-0.36'
-    /* Location of Java */
-    JAVA = '/usr/lib/jvm/java-7-openjdk-amd64/bin/java'
-    BBMAP_JAVA= "/usr/local/bbmap/jni/"
-    BBMAP_current = "/usr/local/bbmap/current/"
-    CLUMPIFY = "/usr/lib/jvm/java-7-openjdk-amd64/bin/java -ea -cp /usr/local/bbmap/current/ clump.Clumpify"
-}
-
-
-process {
-  process.executor='pbs'
-  process.container = 'shub://EnriqueDoster/MEG-summit-assembly:latest'
-  maxForks = 30                 // The maximum number of forks a single process is allowed to spawn
-  withName:RunQC {
-      clusterOptions='-N=QC%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:QCStats {
-      clusterOptions='-N=QCstats%j -l walltime=05:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BuildHostIndex {
-      clusterOptions='-N=hostindex%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BuildAMRIndex {
-      clusterOptions='-N=AMRindex%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:DedupReads {
-      clusterOptions='-N=dedup%j  -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AlignReadsToHost {
-      clusterOptions='-N=AlignHost%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:RemoveHostDNA  {
-      clusterOptions='-N=RMHost%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:HostRemovalStats {
-      clusterOptions='-N=hoststats%j -l walltime=05:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BAMToFASTQ {
-      clusterOptions='-N=BAMFastq%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AssembleReads{
-      clusterOptions='-N=assembly%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:HMM_amr {
-      clusterOptions='-N=HMM_amr%j -l procs=15 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AlignDedupedToContigs {
-      clusterOptions='-N=bwa_contig%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AlignToContigs {
-      clusterOptions='-N=bwa_contig%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:HMMcontig_count {
-      clusterOptions='-N=HMMcount%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AlignDedupSNPToAMR {
-      clusterOptions='-N=alignAMR%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AlignToAMR {
-      clusterOptions='-N=alignAMR%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:DedupRunResistome {
-      clusterOptions='-N=resistome%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:RunResistome {
-      clusterOptions='-N=resistome%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:RunFreebayes {
-      clusterOptions='-N=freebayes%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:RunRarefaction {
-      clusterOptions='-N=rarefaction%j -l walltime=23:59:00 -l procs=12'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:RunSNPFinder {
-      clusterOptions='-N=SNPfinder%j -l procs=12 -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:AMRLongToWide {
-      clusterOptions='-N=LtoWide%j -l walltime=05:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPAlignToAMR {
-      clusterOptions='-N=SNPAlignToAMR%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPRunResistome {
-      clusterOptions='-N=SNPresistome%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPRunRarefaction {
-      clusterOptions='-N=SNPrarefaction%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPconfirmation {
-      clusterOptions='-N=SNPconfirmation%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPgene_alignment {
-      clusterOptions='-N=SNPalignment%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPRunFreebayes {
-      clusterOptions='-N=SNPfreebayes%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPRunSNPFinder {
-      clusterOptions='-N=SNPsnpfinder%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SNPAMRLongToWide {
-      clusterOptions='-N=SNPLongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:DedupNonSNPAMRLongToWide {
-      clusterOptions='-N=DedupNonSNPLongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:HMMAMRLongToWide {
-      clusterOptions='-N=HMM_LongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SamDedupRunResistome {
-      clusterOptions='-N=SamDedupSNPresistome%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:SamDedupAMRLongToWide {
-      clusterOptions='-N=SamDedup_LongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:Samtools_dedup_HMMcontig_count {
-      clusterOptions='-N=SamDedupSNPresistome%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:Samtools_dedup_HMMAMRLongToWide {
-      clusterOptions='-N=SamDedup_LongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BBmapDedupAlignToAMR {
-      clusterOptions='-N=BBmapDedupAlignToAMR%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BBmapDedupRunResistome {
-      clusterOptions='-N=BBmapDedupRunResistome%j -l walltime=23:59:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-  withName:BBmapDedupAMRLongToWide {
-      clusterOptions='-N=BBmapDedupAMRLongToWide -l walltime=5:00:00 -q small'
-      module='java/jdk1.8.0_144:singularity/current'
-  }
-}