diff --git a/.gitignore b/.gitignore
index 7ec8546e42..2c63d79039 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,12 +1,13 @@
-data/chr17_testdata
-Annotation
+Annotation/
+data/chr17_testdata/
 Preprocessing/
-Reports/
 References/
+Reports/
 VariantCalling/
 work/
 .*swp
 .nextflow*
+*.img
+*.tar.gz
 timeline.html*
 trace.txt*
-*.tar.gz
diff --git a/.travis.yml b/.travis.yml
index c28f739da0..77be1bb5c7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,11 +11,11 @@ env:
   - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
   - NXF_VER=0.25.6 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
   - NXF_VER=0.25.6 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
-  - NXF_VER=0.25.6 PROFILE=docker TEST=BUILDCONTAINERS TOOL_INSTALL=nextflow
   - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=RECALIBRATE TOOL_INSTALL=all
   - NXF_VER=0.25.6 PROFILE=docker TEST=RECALIBRATE TOOL_INSTALL=nextflow
   - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=REALIGN TOOL_INSTALL=all
   - NXF_VER=0.25.6 PROFILE=docker TEST=REALIGN TOOL_INSTALL=nextflow
+  - NXF_VER=0.25.6 PROFILE=docker TEST=BUILDCONTAINERS TOOL_INSTALL=nextflow
   - NXF_VER=0.25.6 SGT_VER=2.3.1 PROFILE=singularity TEST=MAPPING TOOL_INSTALL=all
   - NXF_VER=0.25.6 PROFILE=docker TEST=MAPPING TOOL_INSTALL=nextflow
 
diff --git a/README.md b/README.md
index 3198ed7bab..22d449cfdf 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,6 @@
 
 [![caw version][version-badge]][version-link] [![License][license-badge]][license-link] [![nextflow version][nextflow-badge]][nextflow-link] [![Join the chat at https://gitter.im/SciLifeLab/CAW][gitter-badge]][gitter-link] [![Travis status][travis-badge]][travis-link]
 
-
 CAW is a complete open source pipeline to detect somatic variants from WGS data developed at the [National Genomics Infastructure][ngi-link] at [SciLifeLab Stockholm][scilifelab-stockholm-link], Sweden and [National Bioinformatics Infastructure Sweden][nbis-link] at [SciLifeLab][scilifelab-link].
 
 The pipeline uses [Nextflow][nextflow-link], a bioinformatics domain specific language for workflow building and [Singularity](http://singularity.lbl.gov/), a container technology specific for high-performance computing.
diff --git a/buildContainers.nf b/buildContainers.nf
index 2c19dac666..77871bb3f6 100644
--- a/buildContainers.nf
+++ b/buildContainers.nf
@@ -36,7 +36,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.2'
+version = '1.2.3'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
@@ -58,6 +58,22 @@ if (params.version) exit 0, versionMessage()
 if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
 if (!checkUppmaxProject()) exit 1, "No UPPMAX project ID found! Use --project <UPPMAX Project ID>"
 
+// Default params:
+// Such params are overridden by command line or configuration definitions
+
+// containerPath is empty
+params.containerPath = ''
+// all containers to be build
+params.containers = 'all'
+// Docker will not be used
+params.docker = false
+// Containers will not be pushed on DockerHub
+params.push = false
+// DockerHub repository is maxulysse
+params.repository = 'maxulysse'
+// Singularity will not be used
+params.singularity = false
+
 verbose = params.verbose
 containersList = defineContainersList()
 containers = params.containers.split(',').collect {it.trim()}
@@ -67,7 +83,9 @@ push = params.docker && params.push ? true : false
 repository = params.repository
 tag = params.tag ? params.tag : version
 singularity = params.singularity ? true : false
-singularityPublishDir = params.singularity && params.singularityPublishDir ? params.singularityPublishDir : "."
+containerPath = params.singularity && params.containerPath ? params.containerPath : "."
+
+if (!docker && !singularity) exit 1, 'No builder choose, specify --docker or --singularity, see --help for more information'
 
 if (!checkContainers(containers,containersList)) exit 1, 'Unknown container(s), see --help for more information'
 
@@ -106,7 +124,7 @@ if (verbose) dockerContainersBuilt = dockerContainersBuilt.view {
 process PullSingularityContainers {
   tag {repository + "/" + container + ":" + tag}
 
-  publishDir singularityPublishDir, mode: 'move'
+  publishDir containerPath, mode: 'move'
 
   input:
     val container from singularityContainers
@@ -188,6 +206,8 @@ def checkParams(it) {
     'callName',
     'contact-mail',
     'contactMail',
+    'container-path',
+    'containerPath',
     'containers',
     'docker',
     'genome',
@@ -205,9 +225,7 @@ def checkParams(it) {
     'sampleDir',
     'single-CPUMem',
     'singleCPUMem',
-    'singularity-publish-dir',
     'singularity',
-    'singularityPublishDir',
     'step',
     'tag',
     'test',
@@ -241,7 +259,6 @@ def defineContainersList(){
     'snpeff',
     'snpeffgrch37',
     'snpeffgrch38',
-    'vep',
     'vepgrch37',
     'vepgrch38'
     ]
@@ -258,7 +275,7 @@ def helpMessage() {
   log.info "    Usage:"
   log.info "       nextflow run SciLifeLab/buildContainers.nf [--docker] [--push]"
   log.info "          [--containers <container1...>] [--singularity]"
-  log.info "          [--singularityPublishDir <path>]"
+  log.info "          [--containerPath <path>]"
   log.info "          [--tag <tag>] [--repository <repository>]"
   log.info "    Example:"
   log.info "      nextflow run . --docker --containers multiqc,fastqc"
@@ -275,7 +292,7 @@ def helpMessage() {
   log.info "    --repository: Build containers under given repository"
   log.info "       Default: maxulysse"
   log.info "    --singularity: Build containers using Singularity"
-  log.info "    --singularityPublishDir: Select where to download containers"
+  log.info "    --containerPath: Select where to download containers"
   log.info "       Default: $PWD"
   log.info "    --tag`: Build containers using given tag"
   log.info "       Default (version number): " + version
diff --git a/buildReferences.nf b/buildReferences.nf
index 950f9059c0..b2e3092d01 100644
--- a/buildReferences.nf
+++ b/buildReferences.nf
@@ -39,7 +39,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.2'
+version = '1.2.3'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
@@ -61,8 +61,14 @@ if (params.version) exit 0, versionMessage()
 if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
 if (!checkUppmaxProject()) exit 1, "No UPPMAX project ID found! Use --project <UPPMAX Project ID>"
 
+// Default params:
+// Such params are overridden by command line or configuration definitions
+
+// No download
 params.download = false
-params.refDir = ""
+// refDir is empty
+params.refDir = ''
+
 verbose = params.verbose
 download = params.download ? true : false
 
@@ -309,6 +315,8 @@ def checkParams(it) {
     'callName',
     'contact-mail',
     'contactMail',
+    'container-path',
+    'containerPath',
     'containers',
     'docker',
     'download',
@@ -331,9 +339,7 @@ def checkParams(it) {
     'sampleDir',
     'single-CPUMem',
     'singleCPUMem',
-    'singularity-publish-dir',
     'singularity',
-    'singularityPublishDir',
     'step',
     'tag',
     'test',
diff --git a/configuration/containers.config b/configuration/containers.config
new file mode 100644
index 0000000000..d8015cca13
--- /dev/null
+++ b/configuration/containers.config
@@ -0,0 +1,44 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ * Nextflow config file for CAW project
+ * -------------------------------------------------
+ * Images for every process
+ * All images will be pulled automatically
+ * -------------------------------------------------
+ */
+
+process {
+  $BuildBWAindexes.container          = "${params.repository}/caw:${params.tag}"
+  $BuildPicardIndex.container         = "${params.repository}/picard:${params.tag}"
+  $BuildSAMToolsIndex.container       = "${params.repository}/caw:${params.tag}"
+  $BuildVCFIndex.container            = "${params.repository}/igvtools:${params.tag}"
+  $ConcatVCF.container                = "${params.repository}/caw:${params.tag}"
+  $CreateRecalibrationTable.container = "${params.repository}/gatk:${params.tag}"
+  $IndelRealigner.container           = "${params.repository}/gatk:${params.tag}"
+  $MapReads.container                 = "${params.repository}/caw:${params.tag}"
+  $MarkDuplicates.container           = "${params.repository}/picard:${params.tag}"
+  $MergeBams.container                = "${params.repository}/caw:${params.tag}"
+  $RealignerTargetCreator.container   = "${params.repository}/gatk:${params.tag}"
+  $RecalibrateBam.container           = "${params.repository}/gatk:${params.tag}"
+  $RunAlleleCount.container           = "${params.repository}/runallelecount:${params.tag}"
+  $RunAscat.container                 = "${params.repository}/r-base:${params.tag}"
+  $RunBamQC.container                 = "${params.repository}/qualimap:${params.tag}"
+  $RunBcftoolsStats.container         = "${params.repository}/caw:${params.tag}"
+  $RunConvertAlleleCounts.container   = "${params.repository}/r-base:${params.tag}"
+  $RunFastQC.container                = "${params.repository}/fastqc:${params.tag}"
+  $RunFreeBayes.container             = "${params.repository}/freebayes:${params.tag}"
+  $RunGenotypeGVCFs.container         = "${params.repository}/gatk:${params.tag}"
+  $RunHaplotypecaller.container       = "${params.repository}/gatk:${params.tag}"
+  $RunManta.container                 = "${params.repository}/caw:${params.tag}"
+  $RunMultiQC.container               = "${params.repository}/multiqc:${params.tag}"
+  $RunMutect1.container               = "${params.repository}/mutect1:${params.tag}"
+  $RunMutect2.container               = "${params.repository}/gatk:${params.tag}"
+  $RunSamtoolsStats.container         = "${params.repository}/caw:${params.tag}"
+  $RunSingleManta.container           = "${params.repository}/caw:${params.tag}"
+  $RunSingleStrelka.container         = "${params.repository}/caw:${params.tag}"
+  $RunSnpeff.container = {params.genome == "GRCh38" ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
+  $RunStrelka.container               = "${params.repository}/caw:${params.tag}"
+  $RunVEP.container = {params.genome == "GRCh38" ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
+}
diff --git a/configuration/docker.config b/configuration/docker.config
index 368e6132fd..69711042ad 100644
--- a/configuration/docker.config
+++ b/configuration/docker.config
@@ -14,36 +14,5 @@ docker {
   fixOwnership = true
 }
 
-process {
-  $BuildBWAindexes.container          = 'maxulysse/caw:1.2.1'
-  $BuildPicardIndex.container         = 'maxulysse/picard:1.2.1'
-  $BuildSAMToolsIndex.container       = 'maxulysse/caw:1.2.1'
-  $BuildVCFIndex.container            = 'maxulysse/igvtools:1.2.1'
-  $ConcatVCF.container                = 'maxulysse/caw:1.2.1'
-  $CreateRecalibrationTable.container = 'maxulysse/gatk:1.2.1'
-  $IndelRealigner.container           = 'maxulysse/gatk:1.2.1'
-  $MapReads.container                 = 'maxulysse/caw:1.2.1'
-  $MarkDuplicates.container           = 'maxulysse/picard:1.2.1'
-  $MergeBams.container                = 'maxulysse/caw:1.2.1'
-  $RealignerTargetCreator.container   = 'maxulysse/gatk:1.2.1'
-  $RecalibrateBam.container           = 'maxulysse/gatk:1.2.1'
-  $RunAlleleCount.container           = 'maxulysse/runallelecount:1.2.1'
-  $RunAscat.container                 = 'maxulysse/r-base:1.2.1'
-  $RunBamQC.container                 = 'maxulysse/qualimap:1.2.1'
-  $RunBcftoolsStats.container         = 'maxulysse/caw:1.2.1'
-  $RunConvertAlleleCounts.container   = 'maxulysse/r-base:1.2.1'
-  $RunFastQC.container                = 'maxulysse/fastqc:1.2.1'
-  $RunFreeBayes.container             = 'maxulysse/freebayes:1.2.1'
-  $RunGenotypeGVCFs.container         = 'maxulysse/gatk:1.2.1'
-  $RunHaplotypecaller.container       = 'maxulysse/gatk:1.2.1'
-  $RunManta.container                 = 'maxulysse/caw:1.2.1'
-  $RunMultiQC.container               = 'maxulysse/multiqc:1.2.1'
-  $RunMutect1.container               = 'maxulysse/mutect1:1.2.1'
-  $RunMutect2.container               = 'maxulysse/gatk:1.2.1'
-  $RunSamtoolsStats.container         = 'maxulysse/caw:1.2.1'
-  $RunSingleManta.container           = 'maxulysse/caw:1.2.1'
-  $RunSingleStrelka.container         = 'maxulysse/caw:1.2.1'
-  $RunSnpeff.container = {params.genome == "GRCh38" ? 'maxulysse/snpeffgrch38:1.2.1' : 'maxulysse/snpeffgrch37:1.2.1'}
-  $RunStrelka.container               = 'maxulysse/caw:1.2.1'
-  $RunVEP.container = {params.genome == "GRCh38" ? 'maxulysse/vepgrch38:1.2.1' : 'maxulysse/vepgrch37:1.2.1'}
-}
+params.repository='maxulysse'
+params.tag='1.2.3'
diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
index d1b05de5e0..4fb21e0ff2 100644
--- a/configuration/singularity-path.config
+++ b/configuration/singularity-path.config
@@ -12,39 +12,43 @@ vim: syntax=groovy
 
 singularity {
   enabled = true
+  runOptions = "--bind /scratch"
 }
 
+params.containerPath='containers'
+params.tag='1.2.3'
+
 process {
-  $BuildBWAindexes.container          = 'containers/caw-1.2.1.img'
-  $BuildPicardIndex.container         = 'containers/picard-1.2.1.img'
-  $BuildSAMToolsIndex.container       = 'containers/caw-1.2.1.img'
-  $BuildVCFIndex.container            = 'containers/igvtools-1.2.1.img'
-  $ConcatVCF.container                = 'containers/caw-1.2.1.img'
-  $CreateRecalibrationTable.container = 'containers/gatk-1.2.1.img'
-  $GenerateMultiQCconfig.container    = 'containers/multiqc-1.2.1.img'
-  $IndelRealigner.container           = 'containers/gatk-1.2.1.img'
-  $MapReads.container                 = 'containers/caw-1.2.1.img'
-  $MarkDuplicates.container           = 'containers/picard-1.2.1.img'
-  $MergeBams.container                = 'containers/caw-1.2.1.img'
-  $RealignerTargetCreator.container   = 'containers/gatk-1.2.1.img'
-  $RecalibrateBam.container           = 'containers/gatk-1.2.1.img'
-  $RunAlleleCount.container           = 'containers/runallelecount-1.2.1.img'
-  $RunAscat.container                 = 'containers/r-base-1.2.1.img'
-  $RunBamQC.container                 = 'containers/qualimap-1.2.1.img'
-  $RunBcftoolsStats.container         = 'containers/caw-1.2.1.img'
-  $RunConvertAlleleCounts.container   = 'containers/r-base-1.2.1.img'
-  $RunFastQC.container                = 'containers/fastqc-1.2.1.img'
-  $RunFreeBayes.container             = 'containers/freebayes-1.2.1.img'
-  $RunGenotypeGVCFs.container         = 'containers/gatk-1.2.1.img'
-  $RunHaplotypecaller.container       = 'containers/gatk-1.2.1.img'
-  $RunManta.container                 = 'containers/caw-1.2.1.img'
-  $RunMultiQC.container               = 'containers/multiqc-1.2.1.img'
-  $RunMutect1.container               = 'containers/mutect1-1.2.1.img'
-  $RunMutect2.container               = 'containers/gatk-1.2.1.img'
-  $RunSamtoolsStats.container         = 'containers/caw-1.2.1.img'
-  $RunSingleManta.container           = 'containers/caw-1.2.1.img'
-  $RunSingleStrelka.container         = 'containers/caw-1.2.1.img'
-  $RunSnpeff.container                = {params.genome == "GRCh38" ? 'containers/snpeffgrch38-1.2.1.img' : 'containers/snpeffgrch37-1.2.1.img'}
-  $RunStrelka.container               = 'containers/caw-1.2.1.img'
-  $RunVEP.container                   = {params.genome == "GRCh38" ? 'containers/vepgrch38-1.2.1.img' : 'containers/vepgrch37-1.2.1.img'}
+  $BuildBWAindexes.container          = "${params.containerPath}/caw-${params.tag}.img"
+  $BuildPicardIndex.container         = "${params.containerPath}/picard-${params.tag}.img"
+  $BuildSAMToolsIndex.container       = "${params.containerPath}/caw-${params.tag}.img"
+  $BuildVCFIndex.container            = "${params.containerPath}/igvtools-${params.tag}.img"
+  $ConcatVCF.container                = "${params.containerPath}/caw-${params.tag}.img"
+  $CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
+  $GenerateMultiQCconfig.container    = "${params.containerPath}/multiqc-${params.tag}.img"
+  $IndelRealigner.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $MapReads.container                 = "${params.containerPath}/caw-${params.tag}.img"
+  $MarkDuplicates.container           = "${params.containerPath}/picard-${params.tag}.img"
+  $MergeBams.container                = "${params.containerPath}/caw-${params.tag}.img"
+  $RealignerTargetCreator.container   = "${params.containerPath}/gatk-${params.tag}.img"
+  $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
+  $RunAscat.container                 = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunBamQC.container                 = "${params.containerPath}/qualimap-${params.tag}.img"
+  $RunBcftoolsStats.container         = "${params.containerPath}/caw-${params.tag}.img"
+  $RunConvertAlleleCounts.container   = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunFastQC.container                = "${params.containerPath}/fastqc-${params.tag}.img"
+  $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
+  $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunHaplotypecaller.container       = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunManta.container                 = "${params.containerPath}/caw-${params.tag}.img"
+  $RunMultiQC.container               = "${params.containerPath}/multiqc-${params.tag}.img"
+  $RunMutect1.container               = "${params.containerPath}/mutect1-${params.tag}.img"
+  $RunMutect2.container               = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunSamtoolsStats.container         = "${params.containerPath}/caw-${params.tag}.img"
+  $RunSingleManta.container           = "${params.containerPath}/caw-${params.tag}.img"
+  $RunSingleStrelka.container         = "${params.containerPath}/caw-${params.tag}.img"
+  $RunSnpeff.container                = {params.genome == "GRCh38" ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
+  $RunStrelka.container               = "${params.containerPath}/caw-${params.tag}.img"
+  $RunVEP.container                   = {params.genome == "GRCh38" ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
 }
diff --git a/configuration/singularity.config b/configuration/singularity.config
index 496d8fb7c9..198b45a9e2 100644
--- a/configuration/singularity.config
+++ b/configuration/singularity.config
@@ -13,36 +13,5 @@ singularity {
   enabled = true
 }
 
-process {
-  $BuildBWAindexes.container          = 'docker://maxulysse/caw:1.2.1'
-  $BuildPicardIndex.container         = 'docker://maxulysse/picard:1.2.1'
-  $BuildSAMToolsIndex.container       = 'docker://maxulysse/caw:1.2.1'
-  $BuildVCFIndex.container            = 'docker://maxulysse/igvtools:1.2.1'
-  $ConcatVCF.container                = 'docker://maxulysse/caw:1.2.1'
-  $CreateRecalibrationTable.container = 'docker://maxulysse/gatk:1.2.1'
-  $IndelRealigner.container           = 'docker://maxulysse/gatk:1.2.1'
-  $MapReads.container                 = 'docker://maxulysse/caw:1.2.1'
-  $MarkDuplicates.container           = 'docker://maxulysse/picard:1.2.1'
-  $MergeBams.container                = 'docker://maxulysse/caw:1.2.1'
-  $RealignerTargetCreator.container   = 'docker://maxulysse/gatk:1.2.1'
-  $RecalibrateBam.container           = 'docker://maxulysse/gatk:1.2.1'
-  $RunAlleleCount.container           = 'docker://maxulysse/runallelecount:1.2.1'
-  $RunAscat.container                 = 'docker://maxulysse/r-base:1.2.1'
-  $RunBamQC.container                 = 'docker://maxulysse/qualimap:1.2.1'
-  $RunBcftoolsStats.container         = 'docker://maxulysse/caw:1.2.1'
-  $RunConvertAlleleCounts.container   = 'docker://maxulysse/r-base:1.2.1'
-  $RunFastQC.container                = 'docker://maxulysse/fastqc:1.2.1'
-  $RunFreeBayes.container             = 'docker://maxulysse/freebayes:1.2.1'
-  $RunGenotypeGVCFs.container         = 'docker://maxulysse/gatk:1.2.1'
-  $RunHaplotypecaller.container       = 'docker://maxulysse/gatk:1.2.1'
-  $RunManta.container                 = 'docker://maxulysse/caw:1.2.1'
-  $RunMultiQC.container               = 'docker://maxulysse/multiqc:1.2.1'
-  $RunMutect1.container               = 'docker://maxulysse/mutect1:1.2.1'
-  $RunMutect2.container               = 'docker://maxulysse/gatk:1.2.1'
-  $RunSamtoolsStats.container         = 'docker://maxulysse/caw:1.2.1'
-  $RunSingleManta.container           = 'docker://maxulysse/caw:1.2.1'
-  $RunSingleStrelka.container         = 'docker://maxulysse/caw:1.2.1'
-  $RunSnpeff.container = {params.genome == "GRCh38" ? 'docker://maxulysse/snpeffgrch38:1.2.1' : 'docker://maxulysse/snpeffgrch37:1.2.1'}
-  $RunStrelka.container               = 'docker://maxulysse/caw:1.2.1'
-  $RunVEP.container = {params.genome == "GRCh38" ? 'docker://maxulysse/vepgrch38:1.2.1' : 'docker://maxulysse/vepgrch37:1.2.1'}
-}
+params.repository='docker://maxulysse'
+params.tag='1.2.3'
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
index d18f507b6e..94df4eb7d3 100644
--- a/configuration/uppmax-localhost.config
+++ b/configuration/uppmax-localhost.config
@@ -18,6 +18,11 @@ params {
   totalMemory = 104.GB // change to 240 on irma
 }
 
+executor {
+  name = 'local'
+  cpus = 16
+}
+
 process {
   // Default process resources
 
diff --git a/containers/fastqc/Dockerfile b/containers/fastqc/Dockerfile
index ad746292fd..65e2fa37b4 100644
--- a/containers/fastqc/Dockerfile
+++ b/containers/fastqc/Dockerfile
@@ -8,10 +8,8 @@ LABEL \
 # Install libraries
 RUN \
   apt-get update && apt-get install -y --no-install-recommends \
-    cpanminus \
     wget \
-  && rm -rf /var/lib/apt/lists/* \
-  && cpanm FindBin
+  && rm -rf /var/lib/apt/lists/*
 
 # Setup ENV variables
 ENV FASTQC_VERSION=0.11.5
diff --git a/containers/freebayes/Dockerfile b/containers/freebayes/Dockerfile
index 5f4ac0be36..afe2bf0313 100644
--- a/containers/freebayes/Dockerfile
+++ b/containers/freebayes/Dockerfile
@@ -17,7 +17,7 @@ RUN \
   && rm -rf /var/lib/apt/lists/*
 
 # Setup ENV variables
-ENV FREEBAYES_VERSION="1.1.0"
+ENV FREEBAYES_VERSION=1.1.0
 
 # Install BCFTools
 RUN \
diff --git a/containers/gatk/Dockerfile b/containers/gatk/Dockerfile
index 97864cd0cf..1cdfaf5dc2 100644
--- a/containers/gatk/Dockerfile
+++ b/containers/gatk/Dockerfile
@@ -5,8 +5,7 @@ LABEL \
   description="GATK image for use in CAW" \
   maintainer="maxime.garcia@scilifelab.se"
 
-ENV \
-GATK_HOME=/usr
+ENV GATK_HOME=/usr
 
 # Create UPPMAX directories
 RUN mkdir /pica /proj /scratch /sw
diff --git a/containers/mutect1/Dockerfile b/containers/mutect1/Dockerfile
index ae0f3ca4dd..7c0d2a3f6e 100644
--- a/containers/mutect1/Dockerfile
+++ b/containers/mutect1/Dockerfile
@@ -8,20 +8,20 @@ LABEL \
 # Install libraries
 RUN \
   apt-get update && apt-get install -y --no-install-recommends \
-  wget \
+    wget \
   && rm -rf /var/lib/apt/lists/*
 
 # Setup ENV variables
 ENV \
-  MUTECT_HOME="/opt/mutect-1.1.5" \
-  MUTECT_VERSION="1.1.5"
+  MUTECT_HOME=/opt/mutect-1.1.5 \
+  MUTECT_VERSION=1.1.5
 
 # Install MuTect1
 RUN \
   wget --quiet -O muTect-${MUTECT_VERSION}-bin.zip \
     https://github.com/broadinstitute/mutect/releases/download/${MUTECT_VERSION}/muTect-${MUTECT_VERSION}-bin.zip \
-  && unzip muTect-${MUTECT_VERSION}-bin.zip -d $MUTECT_HOME \
+  && unzip muTect-${MUTECT_VERSION}-bin.zip -d ${MUTECT_HOME} \
   && rm muTect-${MUTECT_VERSION}-bin.zip \
-&& mv $MUTECT_HOME/muTect-$MUTECT_VERSION.jar $MUTECT_HOME/muTect.jar
+&& mv ${MUTECT_HOME}/muTect-${MUTECT_VERSION}.jar ${MUTECT_HOME}/muTect.jar
 # Create UPPMAX directories
 RUN mkdir /pica /proj /scratch /sw
diff --git a/containers/qualimap/Dockerfile b/containers/qualimap/Dockerfile
index 1ed69957b9..cf0021840f 100644
--- a/containers/qualimap/Dockerfile
+++ b/containers/qualimap/Dockerfile
@@ -8,7 +8,7 @@ LABEL \
 # Install libraries
 RUN \
   apt-get update && apt-get install -y --no-install-recommends \
-  wget \
+    wget \
   && rm -rf /var/lib/apt/lists/*
 
 # Setup ENV variables
diff --git a/containers/runallelecount/Dockerfile b/containers/runallelecount/Dockerfile
index e9d45a9506..3b6ff53b0a 100644
--- a/containers/runallelecount/Dockerfile
+++ b/containers/runallelecount/Dockerfile
@@ -14,14 +14,15 @@ ENV \
 # Install libraries
 RUN \
   apt-get update && apt-get install -y --no-install-recommends \
-  build-essential \
-  ca-certificates \
-  libbz2-dev \
-  liblzma-dev \
-  libncurses5-dev \
-  libncursesw5-dev \
-  wget \
-  zlib1g-dev
+    build-essential \
+    ca-certificates \
+    libbz2-dev \
+    liblzma-dev \
+    libncurses5-dev \
+    libncursesw5-dev \
+    wget \
+    zlib1g-dev \
+  && rm -rf /var/lib/apt/lists/*
 
 # Install alleleCount
 RUN \
diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile
index 3ab0c6d197..8d47a14090 100644
--- a/containers/snpeff/Dockerfile
+++ b/containers/snpeff/Dockerfile
@@ -18,15 +18,15 @@ RUN \
 
 # Setup ENV variables
 ENV \
-  SNPEFF_BIN="snpEff_v4_3r_core.zip" \
-  SNPEFF_HOME="/opt/snpEff"
+  SNPEFF_VERSION=4_3r \
+  SNPEFF_HOME=/opt/snpEff
 
 # Install snpEff
 RUN \
-  wget --quiet -O $SNPEFF_BIN \
-    http://downloads.sourceforge.net/project/snpeff/$SNPEFF_BIN \
-  && unzip $SNPEFF_BIN -d /opt/ \
-  && rm $SNPEFF_BIN
+  wget --quiet -O snpEff_v${SNPEFF_VERSION}_core.zip \
+    http://downloads.sourceforge.net/project/snpeff/snpEff_v${SNPEFF_VERSION}_core.zip \
+  && unzip snpEff_v${SNPEFF_VERSION}_core.zip -d /opt/ \
+  && rm snpEff_v${SNPEFF_VERSION}_core.zip
 
 # Create UPPMAX directories
 RUN mkdir /pica /proj /scratch /sw
diff --git a/containers/vepgrch37/Dockerfile b/containers/vepgrch37/Dockerfile
index 906fb8e21c..9ba17e873c 100644
--- a/containers/vepgrch37/Dockerfile
+++ b/containers/vepgrch37/Dockerfile
@@ -1,4 +1,4 @@
-FROM willmclaren/ensembl-vep:release_90.5
+FROM willmclaren/ensembl-vep:release_90.6
 
 LABEL \
   author="Maxime Garcia" \
@@ -22,4 +22,3 @@ RUN \
 # Create UPPMAX directories
 USER root
 RUN mkdir /pica /proj /scratch /sw
-USER vep
diff --git a/containers/vepgrch38/Dockerfile b/containers/vepgrch38/Dockerfile
index 238e17d4eb..2ae9170e85 100644
--- a/containers/vepgrch38/Dockerfile
+++ b/containers/vepgrch38/Dockerfile
@@ -1,4 +1,4 @@
-FROM willmclaren/ensembl-vep:release_90.5
+FROM willmclaren/ensembl-vep:release_90.6
 
 LABEL \
   author="Maxime Garcia" \
@@ -22,4 +22,3 @@ RUN \
 # Create UPPMAX directories
 USER root
 RUN mkdir /pica /proj /scratch /sw
-USER vep
diff --git a/data/tiny/tiny/normal/tiny_normal_L001_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L001_R1_TEST.fastq.gz
new file mode 100644
index 0000000000..b25487aa91
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L001_R1_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L001_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L001_R2_TEST.fastq.gz
new file mode 100644
index 0000000000..b917c80cef
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L001_R2_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L002_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L002_R1_TEST.fastq.gz
new file mode 100644
index 0000000000..509295fdf7
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L002_R1_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L002_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L002_R2_TEST.fastq.gz
new file mode 100644
index 0000000000..ae0e1e6ee7
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L002_R2_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L004_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L004_R1_TEST.fastq.gz
new file mode 100644
index 0000000000..29e4a3bd15
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L004_R1_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L004_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L004_R2_TEST.fastq.gz
new file mode 100644
index 0000000000..f645870a8f
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L004_R2_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L007_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L007_R1_TEST.fastq.gz
new file mode 100644
index 0000000000..8e3c3d295a
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L007_R1_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L007_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L007_R2_TEST.fastq.gz
new file mode 100644
index 0000000000..d03e2369c0
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L007_R2_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L008_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L008_R1_TEST.fastq.gz
new file mode 100644
index 0000000000..ec28edfb5d
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L008_R1_TEST.fastq.gz differ
diff --git a/data/tiny/tiny/normal/tiny_normal_L008_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_normal_L008_R2_TEST.fastq.gz
new file mode 100644
index 0000000000..f02dc49a05
Binary files /dev/null and b/data/tiny/tiny/normal/tiny_normal_L008_R2_TEST.fastq.gz differ
diff --git a/doc/BUILD.md b/doc/BUILD.md
index 30d75b1f69..22a6638498 100644
--- a/doc/BUILD.md
+++ b/doc/BUILD.md
@@ -8,11 +8,12 @@ All the containers have built in UPPMAX directories, so there is no need to add
 ## Usage
 
 ```bash
-nextflow run . [--docker] [--singularity] [--singularityPublishDir <path>] [--push] [--containers <container1[,container2..]>] [--repository <repository>] [--tag tag]
+nextflow run . [--docker] [--singularity] [--containerPath <path>] [--push] [--containers <container1[,container2..]>] [--repository <repository>] [--tag tag]
 ```
 
 - `--containers`: Choose which containers to build. Default: `all`. Possible values (to separate by commas):
   - `all` -  Build all available containers.
+  - `caw`
   - `fastqc`
   - `freebayes`
   - `gatk`
@@ -21,13 +22,11 @@ nextflow run . [--docker] [--singularity] [--singularityPublishDir <path>] [--pu
   - `mutect1`
   - `picard`
   - `qualimap`
+  - `r-base`
   - `runallelecount`
-  - `runascat`
-  - `runconvertallelecounts`
   - `snpeff` this container serves as a base for `snpeffgrch37` and `snpeffgrch38`
   - `snpeffgrch37`
   - `snpeffgrch38`
-  - `vep` this container serves as a base for `vepgrch37` and `vepgrch38`
   - `vepgrch37`
   - `vepgrch38`
 
@@ -35,7 +34,7 @@ nextflow run . [--docker] [--singularity] [--singularityPublishDir <path>] [--pu
 - `--push`: Push containers to `DockerHub`
 - `--repository`: Build containers under given repository. Default: `maxulysse`
 - `--singularity`: Build containers using `Singularity`.
-- `--singularityPublishDir`: Select where to download containers. Default: `$PWD`
+- `--containerPath`: Select where to download containers. Default: `$PWD`
 - `--tag`: Build containers using given tag. Default is version number.
 
 ## Example
diff --git a/doc/CONFIG.md b/doc/CONFIG.md
index 4f44acad20..a8830a7a0f 100644
--- a/doc/CONFIG.md
+++ b/doc/CONFIG.md
@@ -10,6 +10,12 @@ We provides several configuration files and profiles for CAW. The standard ones
 
 Every configuration file can be modified for your own use. If you want you can specify the use of a config file using `-c <config file>`
 
+### [`containers.config`](../configuration/containers.config)
+
+Contain images for all process.
+Images will be pulled automatically.
+Use in your own profile if needed.
+
 ### [`docker.config`](../configuration/docker.config)
 
 Contain Docker images for all process.
diff --git a/doc/CONTAINERS.md b/doc/CONTAINERS.md
index 5c58c6196e..ff7943f63c 100644
--- a/doc/CONTAINERS.md
+++ b/doc/CONTAINERS.md
@@ -1,5 +1,29 @@
 # Containers
 
+Subsets of all containers can be dowloaded:
+
+For normal-only processing + Reports + HaploTypeCaller, Manta and Strelka:
+ - [caw](#caw-)
+ - [fastqc](#fastqc-)
+ - [gatk](#gatk-)
+ - [multiqc](#multiqc-)
+ - [picard](#picard-)
+ - [qualimap](#qualimap-)
+
+For the rest of the variant callers, you will need also:
+ - [freebayes](#freebayes-)
+ - [mutect1](#mutect1-)
+ - [r-base](#r-base-)
+ - [runallelecount](#runallelecount-)
+
+For annotation for GRCh37, you will need:
+ - [snpeffgrch37](#snpeffgrch37-)
+ - [vepgrch37](#vepgrch37-)
+
+For annotation for GRCh38, you will need:
+ - [snpeffgrch38](#snpeffgrch38-)
+ - [vepgrch38](#vepgrch38-)
+
 A container named after the process is made for each process. If a container can be reused, it will be named after the tool used.
 
 ## caw [![caw-docker status][caw-docker-badge]][caw-docker-link]
@@ -85,13 +109,13 @@ A container named after the process is made for each process. If a container can
 
 ## vepgrch37 [![vepgrch37-docker status][vepgrch37-docker-badge]][vepgrch37-docker-link]
 
-- Based on `willmclaren/ensembl-vep:release_90.5`
+- Based on `willmclaren/ensembl-vep:release_90.6`
 - Contain **[VEP][vep-link]** 90.5
 - Contain GRCh37
 
 ## vepgrch38 [![vepgrch38-docker status][vepgrch38-docker-badge]][vepgrch38-docker-link]
 
-- Based on `willmclaren/ensembl-vep:release_90.5`
+- Based on `willmclaren/ensembl-vep:release_90.6`
 - Contain **[VEP][vep-link]** 90.5
 - Contain GRCh38
 
diff --git a/doc/USAGE.md b/doc/USAGE.md
index bc7cd80c76..316693ec04 100644
--- a/doc/USAGE.md
+++ b/doc/USAGE.md
@@ -86,9 +86,47 @@ Display more information about files being processed.
 
 Display version number and information.
 
+## Containers
+
+### --containerPath `Path to the singularity containers (default=containers/)`
+
+### --repository `Docker-hub repository (default=maxulysse)`
+
+### --tag `tag of the containers to use (default=current version)`
+
+## References
+
+If needed, you can specify each reference file by command line.
+
+### --acLoci `acLoci file`
+
+### --bwaIndex `bwaIndex file`
+
+### --cosmic `cosmic file`
+
+### --cosmicIndex `cosmicIndex file`
+
+### --dbsnp `dbsnp file`
+
+### --dbsnpIndex `dbsnpIndex file`
+
+### --genomeDict `genomeDict file`
+
+### --genomeFile `genomeFile file`
+
+### --genomeIndex `genomeIndex file`
+
+### --intervals `intervals file`
+
+### --knownIndels `knownIndels file`
+
+### --knownIndelsIndex `knownIndelsIndex file`
+
+### --snpeffDb `snpeffDb file`
+
 ## Parameters
 
-Simpler to specify in the config file.
+Simpler to specify in the configuration files, but it's still possible to specify every thing in the command line.
 
 ### --runTime `time`
 
diff --git a/main.nf b/main.nf
index 385129008d..cf4a002bda 100644
--- a/main.nf
+++ b/main.nf
@@ -41,7 +41,6 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - CreateIntervalBeds - Create and sort intervals into bed files
  - RunHaplotypecaller - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
  - RunGenotypeGVCFs - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
- - RunBcftoolsStats - Run BCFTools stats on vcf before annotation
  - RunMutect1 - Run MuTect1 for Variant Calling (Parallelized processes)
  - RunMutect2 - Run MuTect2 for Variant Calling (Parallelized processes)
  - RunFreeBayes - Run FreeBayes for Variant Calling (Parallelized processes)
@@ -53,9 +52,9 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - RunAlleleCount - Run AlleleCount to prepare for ASCAT
  - RunConvertAlleleCounts - Run convertAlleleCounts to prepare for ASCAT
  - RunAscat - Run ASCAT for CNV
+ - RunBcftoolsStats - Run BCFTools stats on vcf before annotation
  - RunSnpeff - Run snpEff for annotation of vcf files
  - RunVEP - Run VEP for annotation of vcf files
- - RunBcftoolsStats - Run BCFTools stats on vcf files
  - GenerateMultiQCconfig - Generate a config file for MultiQC
  - RunMultiQC - Run MultiQC for report and QC
 ================================================================================
@@ -63,7 +62,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.2'
+version = '1.2.3'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
@@ -73,13 +72,39 @@ try {
         throw GroovyException('Nextflow version too old')
     }
 } catch (all) {
-    log.error "====================================================\n" +
+    log.error "============================================================\n" +
               "  Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\n" +
               "  Pipeline execution will continue, but things may break.\n" +
               "  Please update Nextflow.\n" +
               "============================================================"
 }
 
+// Default params:
+// Such params are overridden by command line or configuration definitions
+
+// No tools to annotate
+params.annotateTools = ''
+// No vcf to annotare
+params.annotateVCF = ''
+// For MultiQC reports
+params.callName = ''
+// For MultiQC reports
+params.contactMail = ''
+// GVCF are generated
+params.noGVCF = false
+// Reports are generated
+params.noReports = false
+// No sample is defined
+params.sample = ''
+// No sampleDir is defined
+params.sampleDir = ''
+// Step is mapping
+params.step = 'mapping'
+// Not testing
+params.test = ''
+// No tools to be used
+params.tools = ''
+
 if (params.help) exit 0, helpMessage()
 if (params.version) exit 0, versionMessage()
 if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
@@ -124,9 +149,9 @@ else explicitBqsrNeeded = tools.intersect(['manta', 'mutect1', 'mutect2', 'vardi
 tsvPath = ''
 if (params.sample) tsvPath = params.sample
 
+// No need for tsv file for step annotate
 if (!params.sample && !params.sampleDir) {
   tsvPaths = [
-  'annotate': "$workflow.launchDir/$directoryMap.recalibrated/recalibrated.tsv",
   'mapping': "$workflow.projectDir/data/tsv/tiny.tsv",
   'realign': "$workflow.launchDir/$directoryMap.nonRealigned/nonRealigned.tsv",
   'recalibrate': "$workflow.launchDir/$directoryMap.nonRecalibrated/nonRecalibrated.tsv",
@@ -136,12 +161,12 @@ if (!params.sample && !params.sampleDir) {
 }
 
 // Set up the fastqFiles and bamFiles channels. One of them remains empty
+// Except for step annotate, in which both stay empty
 fastqFiles = Channel.empty()
 bamFiles = Channel.empty()
 if (tsvPath) {
   tsvFile = file(tsvPath)
   switch (step) {
-    case 'annotate': bamFiles = extractBams(tsvFile); break
     case 'mapping': fastqFiles = extractFastq(tsvFile); break
     case 'realign': bamFiles = extractBams(tsvFile); break
     case 'recalibrate': bamFiles = extractRecal(tsvFile); break
@@ -152,7 +177,7 @@ if (tsvPath) {
   if (step != 'mapping') exit 1, '--sampleDir does not support steps other than "mapping"'
   fastqFiles = extractFastqFromDir(params.sampleDir)
   tsvFile = params.sampleDir  // used in the reports
-} else exit 1, 'No sample were defined, see --help'
+} else if (step != 'annotate') exit 1, 'No sample were defined, see --help'
 
 if (step == 'mapping') {
   (patientGenders, fastqFiles) = extractGenders(fastqFiles)
@@ -633,7 +658,11 @@ process RunBamQC {
 
     script:
     """
-    qualimap --java-mem-size=${task.memory.toGiga()}G bamqc -bam $bam -outdir $idSample -outformat HTML
+    qualimap --java-mem-size=${task.memory.toGiga()}G \
+    bamqc \
+    -bam $bam \
+    -outdir $idSample \
+    -outformat HTML
     """
 }
 
@@ -1383,7 +1412,7 @@ if (step == 'annotate' && annotateVCF == []) {
 
 vcfNotToAnnotate.close()
 
-(vcfForBCF, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(3)
+(vcfForBCFtools, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(3)
 
 process RunBcftoolsStats {
   tag {vcf}
@@ -1391,7 +1420,7 @@ process RunBcftoolsStats {
   publishDir directoryMap.bcftoolsStats, mode: 'copy'
 
   input:
-    set variantCaller, file(vcf) from vcfForBCF
+    set variantCaller, file(vcf) from vcfForBCFtools
 
   output:
     file ("${vcf.baseName}.bcf.tools.stats.out") into bcfReport
@@ -1419,7 +1448,7 @@ process RunSnpeff {
     val snpeffDb from Channel.value(params.genomes[params.genome].snpeffDb)
 
   output:
-    set file("${vcf.baseName}.ann.vcf"), file("${vcf.baseName}_snpEff_genes.txt"), file("${vcf.baseName}_snpEff.csv"), file("${vcf.baseName}_snpEff_summary.html") into snpeffReport
+    set file("${vcf.baseName}.snpEff.ann.vcf"), file("${vcf.baseName}.snpEff.genes.txt"), file("${vcf.baseName}.snpEff.csv"), file("${vcf.baseName}.snpEff.summary.html") into snpeffReport
 
   when: 'snpeff' in tools
 
@@ -1428,13 +1457,14 @@ process RunSnpeff {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$SNPEFF_HOME/snpEff.jar \
   $snpeffDb \
-  -csvStats ${vcf.baseName}_snpEff.csv \
-  -v -cancer \
+  -csvStats ${vcf.baseName}.snpEff.csv \
+  -nodownload \
+  -cancer \
+  -v \
   ${vcf} \
-  > ${vcf.baseName}.ann.vcf
+  > ${vcf.baseName}.snpEff.ann.vcf
 
-  mv snpEff_summary.html ${vcf.baseName}_snpEff_summary.html
-  mv ${vcf.baseName}_snpEff.genes.txt ${vcf.baseName}_snpEff_genes.txt
+  mv snpEff_summary.html ${vcf.baseName}.snpEff.summary.html
   """
 }
 
@@ -1452,45 +1482,25 @@ process RunVEP {
     set variantCaller, file(vcf) from vcfForVep
 
   output:
-    set file("${vcf.baseName}.ann.vcf"), file("${vcf.baseName}*summary*") into vepReport
+    set file("${vcf.baseName}.vep.ann.vcf"), file("${vcf.baseName}.vep.summary.html") into vepReport
 
   when: 'vep' in tools
 
   script:
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
-  if (!workflow.container.isEmpty())  // test whether running in docker
   """
   vep \
   -i $vcf \
+  -o ${vcf.baseName}.vep.ann.vcf \
+  --stats_file ${vcf.baseName}.vep.summary.html \
+  --cache \
+  --everything \
+  --filter_common \
   --format vcf \
-  --sift b \
-  --polyphen b \
-  --symbol \
-  --numbers \
-  --biotype \
-  --total_length \
-  -o ${vcf.baseName}.ann.vcf \
-  --vcf \
-  -offline \
-  --fields Consequence,Codons,Amino_acids,Gene,SYMBOL,Feature,EXON,PolyPhen,SIFT,Protein_position,BIOTYPE
-  """
-  else
-  """
-  variant_effect_predictor.pl \
-  -i $vcf \
-  --vcf \
-  --format vcf \
-  --sift b \
-  --polyphen b \
-  --symbol \
-  --numbers \
-  --biotype \
+  --offline \
+  --pick \
   --total_length \
-  -o ${vcf.baseName}.ann.vcf \
-  --cache --dir_cache /sw/data/uppnex/vep/89 \
-  --assembly $genome \
-  --fields Consequence,Codons,Amino_acids,Gene,SYMBOL,Feature,EXON,PolyPhen,SIFT,Protein_position,BIOTYPE \
-  -offline
+  --vcf
   """
 }
 
@@ -1510,7 +1520,9 @@ process GenerateMultiQCconfig {
   when: reports
 
   script:
-  annotateString = annotateTools ? "- Annotate on : ${annotateTools.join(", ")}" : ''
+  annotateToolString = annotateTools ? "- Annotate on : ${annotateTools.join(", ")}" : ''
+  annotateVCFstring = annotateVCF ? "- Annotate on : ${annotateVCF.join(", ")}" : ''
+  tsvString = step != 'annotate' ? "- TSV file: ${tsvFile}" : ''
   """
   touch multiqc_config.yaml
   echo "custom_logo: $baseDir/doc/images/CAW_logo.png" >> multiqc_config.yaml
@@ -1518,14 +1530,16 @@ process GenerateMultiQCconfig {
   echo "custom_logo_title: 'Cancer Analysis Workflow'" >> multiqc_config.yaml
   echo "report_header_info:" >> multiqc_config.yaml
   echo "- CAW version: $version" >> multiqc_config.yaml
+  echo "- Contact Name: ${params.callName}" >> multiqc_config.yaml
   echo "- Contact E-mail: ${params.contactMail}" >> multiqc_config.yaml
   echo "- Command Line: ${workflow.commandLine}" >> multiqc_config.yaml
   echo "- Directory: ${workflow.launchDir}" >> multiqc_config.yaml
-  echo "- TSV file: ${tsvFile}" >> multiqc_config.yaml
-  echo "- Genome: "${params.genome} >> multiqc_config.yaml
+  echo ${tsvString} >> multiqc_config.yaml
+    echo "- Genome: "${params.genome} >> multiqc_config.yaml
   echo "- Step: "${step} >> multiqc_config.yaml
   echo "- Tools: "${tools.join(", ")} >> multiqc_config.yaml
-  echo ${annotateString} >> multiqc_config.yaml
+  echo ${annotateToolString} >> multiqc_config.yaml
+  echo ${annotateVCFstring} >> multiqc_config.yaml
   echo "  acLoci      : $referenceMap.acLoci" >> multiqc_config.yaml
   echo "  bwaIndex    : "${referenceMap.bwaIndex.join(", ")} >> multiqc_config.yaml
   echo "  cosmic      : $referenceMap.cosmic" >> multiqc_config.yaml
@@ -1644,6 +1658,8 @@ def checkParams(it) {
     'callName',
     'contact-mail',
     'contactMail',
+    'container-path',
+    'containerPath',
     'containers',
     'cosmic-index',
     'cosmic',
@@ -1679,9 +1695,7 @@ def checkParams(it) {
     'sampleDir',
     'single-CPUMem',
     'singleCPUMem',
-    'singularity-publish-dir',
     'singularity',
-    'singularityPublishDir',
     'step',
     'tag',
     'test',
@@ -2046,11 +2060,12 @@ def minimalInformationMessage() {
   log.info "Project Dir : $workflow.projectDir"
   log.info "Launch Dir  : $workflow.launchDir"
   log.info "Work Dir    : $workflow.workDir"
-  log.info "TSV file    : $tsvFile"
+  if (step != 'annotate') log.info "TSV file    : $tsvFile"
   log.info "Genome      : " + params.genome
   log.info "Step        : " + step
-  if (tools) {log.info "Tools       : " + tools.join(', ')}
-  if (annotateTools) {log.info "Annotate on : " + annotateTools.join(', ')}
+  if (tools) log.info "Tools       : " + tools.join(', ')
+  if (annotateTools) log.info "Annotate on : " + annotateTools.join(', ')
+  if (annotateVCF) log.info "VCF files   : " +annotateVCF.join(',\n    ')
   log.info "Reference files used:"
   log.info "  acLoci      : $referenceMap.acLoci"
   log.info "  bwaIndex    : " + referenceMap.bwaIndex.join(',\n    ')
diff --git a/nextflow.config b/nextflow.config
index 1758f219d0..0144204ccf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,28 +12,9 @@ manifest {
 }
 
 params { // default value for params
-  annotateTools = ''
-  annotateVCF = ''
-  build = false
-  callName = '' // For MultiQC reports
-  contactMail = '' // For MultiQC reports
-  containers = 'all'
-  docker = false
   genome = 'GRCh38'
   help = false
-  noGVCF = false
-  noReports = false
   project = ''
-  push = false
-  repository = 'maxulysse'
-  sample = ''
-  sampleDir = ''
-  singularity = false
-  singularityPublishDir = false
-  step = 'mapping'
-  tag = false
-  test = false
-  tools = ''
   vcflist =''
   verbose = false
   version = false
@@ -72,11 +53,13 @@ profiles {
   docker { // For small testing testing with Docker
     includeConfig 'configuration/travis.config'
     includeConfig 'configuration/docker.config'
+    includeConfig 'configuration/containers.config'
   }
   // Singularity images will be pulled automatically
   singularity { // For small testing
     includeConfig 'configuration/travis.config'
     includeConfig 'configuration/singularity.config'
+    includeConfig 'configuration/containers.config'
   }
 }
 
diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index 82a2c5caba..6da2761064 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -1,38 +1,38 @@
 #!/bin/bash
 set -xeuo pipefail
 
-PROFILE="singularity"
-PUSH=""
-REPOSITORY="--repository maxulysse"
-TAG="1.2.1"
-TOOL="docker"
+PROFILE=singularity
+PUSH=''
+REPOSITORY=maxulysse
+TAG=1.2.3
+TOOL=docker
 
 while [[ $# -gt 0 ]]
 do
-    key="$1"
+    key=$1
     case $key in
-        -r|--repository)
-        REPOSITORY="--repository $2"
-        shift # past argument
-        shift # past value
-        ;;
-        -t|--tag)
-        TAG="--tag $2"
+        -p|--profile)
+        PROFILE=$2
         shift # past argument
         shift # past value
         ;;
-        -p|--profile)
-        PROFILE="$2"
+        --pull)
+        TOOL=singularity
         shift # past argument
-        shift # past value
         ;;
         --push)
         PUSH=--push
         shift # past argument
         ;;
-        --pull)
-        TOOL=singularity
+        -r|--repository)
+        REPOSITORY=$2
         shift # past argument
+        shift # past value
+        ;;
+        -t|--tag)
+        TAG=$2
+        shift # past argument
+        shift # past value
         ;;
         *) # unknown option
         shift # past argument
@@ -42,8 +42,8 @@ done
 
 if [ $TOOL = docker ]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} ${REPOSITORY} ${TAG} --containers caw,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,snpeff
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} ${REPOSITORY} ${TAG} --containers snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers caw,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,snpeff
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity ${REPOSITORY} ${TAG} --singularityPublishDir containers/ --containers caw,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers caw,fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,snpeffgrch37,snpeffgrch38,vepgrch37,vepgrch38
 fi
diff --git a/scripts/skeleton_batch.sh b/scripts/skeleton_batch.sh
index 8468b1651e..8b03efe15c 100644
--- a/scripts/skeleton_batch.sh
+++ b/scripts/skeleton_batch.sh
@@ -1,31 +1,99 @@
 #!/bin/bash
-#SBATCH -A sens2016004
 #SBATCH -p node
 #SBATCH -t 168:00:00
+
 set -xeuo pipefail
-# skeleton script to launch nextflow/singularity jobs with slurm on bianca
-# save as whatever, and launch like:
-# sbatch -J sample-MuTect2 ./whatever.sh sample.tsv MuTect2
-#
-# PARAMETERS:
-#  $1 is the sample TSV file
-#  $2 the tool to run
-#
-# use the default deployed CAW version. "testing" versions should be at /castor/project/proj_nobackup/CAW/testing
-CAW=/castor/project/proj_nobackup/CAW/default
+
+# skeleton script to launch CAW jobs on scratch with sbatch on bianca
+
+GENOME=GRCh38
+SAMPLE=''
+STEP=''
+TOOLS=false
+
+while [[ $# -gt 0 ]]
+do
+  key=$1
+  case $key in
+    -g|--genome)
+    GENOME=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -s|--sample)
+    SAMPLE=$2
+    shift # past argument
+    shift # past value
+    ;;
+    --step)
+    STEP=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -t|--tools)
+    TOOLS=$2
+    shift # past argument
+    shift # past value
+    ;;
+    *) # unknown option
+    shift # past argument
+    ;;
+  esac
+done
+
+# Make a specific prefix for logs (trace + timeline)
 DATE=`date +%Y-%b-%d-%H%M`
-PREFIX=${2}_${DATE}
-ln -fs /castor/project/proj_nobackup/CAW/containers containers
+if [[ $TOOLS ]]
+then
+  PREFIX=${TOOLS}_${DATE}
+else
+  PREFIX=${DATE}
+fi
+
+# Use the default deployed CAW version.
+# Other versions (including testing) are at /castor/project/proj_nobackup/CAW/
+CAW=/castor/project/proj_nobackup/CAW/default
 
-# nextflow specific stuff to save everything on /scratch
+# Link containers
+ln -fs /castor/project/proj_nobackup/CAW/containers containers
 
+# Configure Nextflow to save everything on /scratch
 export NXF_TEMP=/scratch
 export NXF_LAUNCHBASE=/scratch
 export NXF_WORK=/scratch
 export NXF_HOME=/castor/project/proj_nobackup/nextflow
 export PATH=${NXF_HOME}/bin:${PATH}
-nextflow run ${CAW}/main.nf --step skipPreprocessing --tools $2 --sample $1 -with-timeline ${PREFIX}.timeline.html -with-trace ${PREFIX}.trace.txt
+
+# save as whatever, and launch like:
+# sbatch -A [project name] -J sample-MuTect2 ./whatever.sh sample.tsv MuTect2
+
+function run_caw() {
+  nextflow run ${CAW}/main.nf $@ -with-timeline ${PREFIX}.timeline.html -with-trace ${PREFIX}.trace.txt
+}
+
+# MAPPING
+if [[ $STEP == MAPPING ]]
+then
+  run_caw() --sample ${SAMPLE} --step mapping
+fi
+
+# RUN A SPECIFIC TOOL:
+#  -s or --sample the sample TSV file
+#  -t or --tools the tool to run
+# Don't forget to specify the right SNIC project
+# or add as the second line:
+#SBATCH -A [project name]
+
+if [[ $STEP == VARIANTCALLING ]]
+then
+  run_caw() --sample ${SAMPLE} --step variantcalling --tools ${TOOLS}
+fi
 
 # for annotation run
-# sbatch -J sample-Ann ./whatever.sh result.vcf[.gz] snpEff
-# nextflow run ${CAW}/main.nf --step annotate --tools $2 --annotateVCF $1 --sample Preprocessing/Recalibrated/recalibrated.tsv -with-timeline ${PREFIX}.timeline.html -with-trace ${PREFIX}.trace.txt
+# sbatch -A [project name] -J sample-Ann ./whatever.sh result.vcf[.gz] snpEff
+# nextflow run ${CAW}/main.nf --step annotate --tools $2 --annotateVCF $1 --noReports --sample Preprocessing/Recalibrated/recalibrated.tsv -with-timeline ${PREFIX}.timeline.html -with-trace -with-trace ${PREFIX}.trace.txt
+
+if [[ $STEP == ANNOTATE ]]
+then
+  run_caw() --step annotate --tools ${TOOLS} --annotateVCF ${SAMPLE}
+fi
diff --git a/scripts/test.sh b/scripts/test.sh
index 44d8cb023b..ddbba94fd7 100755
--- a/scripts/test.sh
+++ b/scripts/test.sh
@@ -1,39 +1,39 @@
 #!/bin/bash
 set -xeuo pipefail
 
-GENOME="smallGRCh37"
-PROFILE="singularity"
-SAMPLE="data/tsv/tiny.tsv"
-TAG="1.2.1"
-TEST="ALL"
+GENOME=smallGRCh37
+PROFILE=singularity
+SAMPLE=data/tsv/tiny.tsv
+TAG=1.2.3
+TEST=ALL
 TRAVIS=${TRAVIS:-false}
 
 while [[ $# -gt 0 ]]
 do
-  key="$1"
+  key=$1
   case $key in
     -g|--genome)
-    GENOME="$2"
+    GENOME=$2
     shift # past argument
     shift # past value
     ;;
     -p|--profile)
-    PROFILE="$2"
+    PROFILE=$2
     shift # past argument
     shift # past value
     ;;
     -s|--sample)
-    SAMPLE="$2"
+    SAMPLE=$2
     shift # past argument
     shift # past value
     ;;
     -t|--test)
-    TEST="$2"
+    TEST=$2
     shift # past argument
     shift # past value
     ;;
     --tag)
-    TAG="$2"
+    TAG=$2
     shift # past argument
     shift # past value
     ;;
@@ -45,84 +45,74 @@ done
 
 function nf_test() {
   echo "$(tput setaf 1)nextflow run $@ -profile $PROFILE --genome $GENOME -resume --verbose$(tput sgr0)"
-  nextflow run "$@" -profile "$PROFILE" --genome $GENOME -resume --verbose
+  nextflow run $@ -profile $PROFILE --genome $GENOME -resume --verbose
 }
 
 # Build references only for smallGRCh37
-if [[ "$GENOME" == "smallGRCh37" ]] && [[ "$TEST" != "BUILDCONTAINERS" ]]
+if [[ $GENOME == smallGRCh37 ]] && [[ $TEST != BUILDCONTAINERS ]]
 then
   nf_test buildReferences.nf --download
   # Remove images only on TRAVIS
-  if [[ "$PROFILE" == "docker" ]] && [[ "$TRAVIS" == true ]]
+  if [[ $PROFILE == docker ]] && [[ $TRAVIS == true ]]
   then
     docker rmi -f maxulysse/igvtools:${TAG}
-  elif [[ "$PROFILE" == singularity ]] && [[ "$TRAVIS" == true ]]
+  elif [[ $PROFILE == singularity ]] && [[ $TRAVIS == true ]]
   then
     rm -rf work/singularity/igvtools-${TAG}.img
   fi
 fi
 
-if [[ "$TEST" = "MAPPING" ]]
+if [[ ALL,MAPPING,REALIGN,RECALIBRATE =~ $TEST ]]
 then
+  nf_test . --step mapping --sampleDir data/tiny/tiny/normal
   nf_test . --step mapping --sample $SAMPLE
 fi
 
-if [[ "$TEST" = "REALIGN" ]] || [[ "$TEST" = "ALL" ]]
+if [[ ALL,REALIGN =~ $TEST ]]
 then
-  nf_test . --step mapping --sample $SAMPLE
   nf_test . --step realign --noReports
   nf_test . --step realign --tools HaplotypeCaller
   nf_test . --step realign --tools HaplotypeCaller --noReports --noGVCF
 fi
 
-if [[ "$TEST" = "RECALIBRATE" ]] || [[ "$TEST" = "ALL" ]]
+if [[ ALL,RECALIBRATE =~ $TEST ]]
 then
-  nf_test . --step mapping --sample $SAMPLE
   nf_test . --step recalibrate --noReports
   nf_test . --step recalibrate --tools FreeBayes,HaplotypeCaller,MuTect1,MuTect2,Strelka
   # Test whether restarting from an already recalibrated BAM works
   nf_test . --step variantCalling --tools Strelka --noReports
 fi
 
-if [[ "$TEST" = "ANNOTATEVEP" ]] || [[ "$TEST" = "ALL" ]]
+if [[ ALL,ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
 then
   nf_test . --step mapping --sample data/tsv/tiny-single-manta.tsv --tools Manta,Strelka
   nf_test . --step mapping --sample data/tsv/tiny-manta.tsv --tools Manta,Strelka
   nf_test . --step mapping --sample $SAMPLE --tools MuTect2
 
   # Remove images only on TRAVIS
-  if [[ "$PROFILE" == "docker" ]] && [[ "$TRAVIS" == true ]]
+  if [[ $PROFILE == docker ]] && [[ $TRAVIS == true ]]
   then
     docker rmi -f maxulysse/caw:${TAG} maxulysse/fastqc:${TAG} maxulysse/gatk:${TAG} maxulysse/picard:${TAG}
-  elif [[ "$PROFILE" == "singularity" ]] && [[ "$TRAVIS" == true ]]
+  elif [[ $PROFILE == singularity ]] && [[ $TRAVIS == true ]]
   then
     rm -rf work/singularity/caw-${TAG}.img work/singularity/fastqc-${TAG}.img work/singularity/gatk-${TAG}.img work/singularity/picard-${TAG}.img
   fi
-  nf_test . --step annotate --tools VEP --annotateTools Manta,Strelka
-  nf_test . --step annotate --tools VEP --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz,VariantCalling/Manta/Manta_9876T_vs_1234N.somaticSV.vcf.gz --noReports
-  nf_test . --step annotate --tools VEP --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz --noReports
-fi
-
-if [[ "$TEST" = "ANNOTATESNPEFF" ]] || [[ "$TEST" = "ALL" ]]
-then
-  nf_test . --step mapping --sample data/tsv/tiny-single-manta.tsv --tools Manta,Strelka
-  nf_test . --step mapping --sample data/tsv/tiny-manta.tsv --tools Manta,Strelka
-  nf_test . --step mapping --sample $SAMPLE --tools MuTect2
-
-  # Remove images only on TRAVIS
-  if [[ "$PROFILE" == "docker" ]] && [[ "$TRAVIS" == true ]]
+  if [[ $TEST = ANNOTATESNPEFF ]]
   then
-    docker rmi -f maxulysse/caw:${TAG} maxulysse/fastqc:${TAG} maxulysse/gatk:${TAG} maxulysse/picard:${TAG}
-  elif [[ "$PROFILE" == "singularity" ]] && [[ "$TRAVIS" == true ]]
+    ANNOTATOR=snpEFF
+  elif [[ $TEST = ANNOTATEVEP ]]
   then
-    rm -rf work/singularity/caw-${TAG}.img work/singularity/fastqc-${TAG}.img work/singularity/gatk-${TAG}.img work/singularity/picard-${TAG}.img
+    ANNOTATOR=VEP
+  elif  [[ $TEST = ALL ]]
+  then
+    ANNOTATOR=snpEFF,VEP
   fi
-  nf_test . --step annotate --tools snpEff --annotateTools Manta,Strelka
-  nf_test . --step annotate --tools snpEff --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz,VariantCalling/Manta/Manta_9876T_vs_1234N.somaticSV.vcf.gz --noReports
-  nf_test . --step annotate --tools snpEff --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz --noReports
+  nf_test . --step annotate --tools ${ANNOTATOR} --annotateTools Manta,Strelka
+  nf_test . --step annotate --tools ${ANNOTATOR} --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz,VariantCalling/Manta/Manta_9876T_vs_1234N.somaticSV.vcf.gz --noReports
+  nf_test . --step annotate --tools ${ANNOTATOR} --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz --noReports
 fi
 
-if [[ "$TEST" = "BUILDCONTAINERS" ]] || [[ "$TEST" = "ALL" ]]
+if [[ ALL,BUILDCONTAINERS =~ $TEST ]]
 then
   nf_test buildContainers.nf --docker --containers caw,fastqc,gatk,igvtools,multiqc,mutect1,picard,qualimap,runallelecount,r-base,snpeff
 fi