diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 0000000000..1bfb75a86c
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,25 @@
+# CAW Contributing Guidelines
+
+Hi there! Many thanks for taking an interest in improving CAW.
+
+We try to manage the required tasks for CAW using GitHub issues, you probably came to this page when creating one. Please use the prefilled template to save time.
+
+However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
+
+> If you need help using CAW then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/SciLifeLab/CAW
+
+## Contribution workflow
+If you'd like to write some code for CAW, the standard workflow
+is as follows:
+
+1. Check that there isn't already an issue about your idea in the
+   [CAW issues](https://github.com/SciLifeLab/CAW/issues) to avoid
+   duplicating work.
+    * Feel free to add a new issue here for the same reason.
+2. Fork the CAW repository to your GitHub account
+3. Make the necessary changes / additions within your forked repository
+4. Submit a Pull Request against the master branch and wait for the code to be reviewed and merged.
+
+If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
+
+For further information/help, please consult the [CAW documentation](https://github.com/SciLifeLab/CAW#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/SciLifeLab/CAW) or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
new file mode 100644
index 0000000000..9bf1ceb308
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE.md
@@ -0,0 +1,43 @@
+<!--
+Hi there!
+
+Many thanks for creating a CAW issue.
+
+Most issues fall into two categories: either you're reporting a problem with CAW or you'd like a change/improvement.
+
+To make sure that you include all of the information needed, please use the template below, you can delete what is not needed.
+
+Please try to include all you can.
+
+You can also delete this entire thing and just type :)
+-->
+
+## Expected Behavior
+<!--
+If you're describing a bug, tell us what should happen
+If you're suggesting a change/improvement, tell us how you think it should work
+-->
+
+## Current Behavior
+<!---
+If describing a bug, tell us what actually happened
+If suggesting a change/improvement, explain the difference from current behavior
+-->
+
+## Possible Solution
+<!---
+Not obligatory, but suggest a fix/reason for the bug,
+or ideas how to implement the addition or change
+-->
+
+## Context (for bugs)
+<!---
+Providing context helps us coming up with a solution
+Include as many relevant details about the environment you experienced the bug in
+-->
+- **CAW `nextflow.log`:**
+  <!-- Re-execute the command line that resulted in a bug with --verbose and -resume and join the .nextflow.log -->
+  - [please drag and drop the `.nextflow.log` file that will help understand the error here]
+- **CAW `input.TSV`:**
+  <!-- Anonymize your TSV file if necessary and join it too  -->
+  - [please drag and drop the `TSV` file that will help reproduce or understand the error here]
diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
new file mode 100644
index 0000000000..21378aebba
--- /dev/null
+++ b/.github/RELEASE_CHECKLIST.md
@@ -0,0 +1,21 @@
+# Release checklist
+This checklist is for our own reference
+
+1. Check that everything is up to date and ready to go
+2. Increase version numbers.
+3. Update version numbers in code: `main.nf`, `buildContainers.nf`, `buildReferences.nf`
+4. If any changes on any containers, match the tag to current version `docker.config`, `singularity.config`, `singularity-path.config`.
+5. Build, and get the containers.
+  - `./scripts/do_all.sh --push`
+  - `./scripts/do_all.sh --pull`
+6. Test against sample data.
+  - Check for any command line errors
+  - Check version numbers are printed correctly
+  - `./scripts/test.sh -p docker`
+  - `./scripts/test.sh -p singularity`
+  - `./scripts/test.sh -p singularityPath`
+7. Commit and push version updates
+8. Make a [release](https://github.com/SciLifeLab/CAW/releases) on GitHub - list PRs as changelog.
+9. Tweet that new version is released
+10. Commit and push. Continue making more awesome :metal:
+11. Have fika :cake:
diff --git a/.gitignore b/.gitignore
index 2c63d79039..44cb9cd70d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,5 +9,6 @@ work/
 .nextflow*
 *.img
 *.tar.gz
+report.html*
 timeline.html*
 trace.txt*
diff --git a/.travis.yml b/.travis.yml
index 77be1bb5c7..e12269ff8d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,19 +8,19 @@ services:
   - docker
 
 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 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
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=RECALIBRATE TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=RECALIBRATE TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=REALIGN TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=REALIGN TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 PROFILE=docker TEST=BUILDCONTAINERS TOOL_INSTALL=nextflow
+  - NXF_VER=0.26.0 SGT_VER=2.3.1 PROFILE=singularity TEST=MAPPING TOOL_INSTALL=all
+  - NXF_VER=0.26.0 PROFILE=docker TEST=MAPPING TOOL_INSTALL=nextflow
 
 install: # Install Nextflow (and Singularity if needed)
   - "./scripts/install.sh --tool $TOOL_INSTALL"
 
 script:
-  - "./scripts/test.sh --profile $PROFILE --test $TEST"
+  - "travis_wait 50 ./scripts/test.sh --profile $PROFILE --test $TEST"
diff --git a/README.md b/README.md
index 22d449cfdf..201b95b478 100644
--- a/README.md
+++ b/README.md
@@ -8,11 +8,19 @@ CAW is a complete open source pipeline to detect somatic variants from WGS data
 
 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.
 
-This pipeline is primarily used with cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se/). However, the pipeline should be able to run on any system that supports Nextflow. The pipeline comes with some configuration for different systems. See the [documentation](#documentation) for more information.
+This pipeline is primarily used with cluster on the Swedish [UPPMAX systems](https://www.uppmax.uu.se/).
+However, the pipeline should be able to run on any system that supports Nextflow.
+The pipeline comes with some configuration for different systems.
+See the [documentation](#documentation) for more information.
 
-We utilize [GATK best practices](https://software.broadinstitute.org/gatk/best-practices/) to align, realign and recalibrate short-read data in parallel for both normal and tumor sample. After these preprocessing steps, several somatic variant callers scan the resulting BAM files: [MuTect1][mutect1-link], [MuTect2][gatk-link] and [Strelka][strelka-link] are used to find somatic SNVs and small indels, also [GATK HaplotyeCaller][gatk-link] for both the normal and the tumor sample. For structural variants we use [Manta][manta-link]. Furthermore, we are applying [ASCAT][ascat-link] to estimate sample heterogeneity, ploidy and CNVs.
+Caw is based on [GATK best practices](https://software.broadinstitute.org/gatk/best-practices/) to align, realign and recalibrate short-read data in parallel for both normal and tumor sample.
+After these preprocessing steps, several somatic variant callers scan the resulting BAM files: [MuTect1][mutect1-link], [MuTect2][gatk-link], [Freebayes][freebayes-link] and [Strelka][strelka-link] are used to find somatic SNVs and small indels, also [GATK HaplotyeCaller][gatk-link] for both the normal and the tumor sample.
+For structural variants we use [Manta][manta-link].
+Furthermore, we are applying [ASCAT][ascat-link] to estimate sample heterogeneity, ploidy and CNVs.
 
-The pipeline can begin the analysis either from raw FASTQ files, only from the realignment step, or directly with any subset of variant callers using recalibrated BAM files. At the end of the analysis the resulting VCF files are merged to facilitate further downstream processing, though results from each caller are also retained. The flow is capable of accommodating additional variant calling software or CNV callers. It is also prepared to process normal, tumor and several relapse samples.
+The pipeline can begin the analysis either from raw FASTQ files, only from the realignment step, or directly with any subset of variant callers using recalibrated BAM files.
+At the end of the analysis the resulting VCF files are merged to facilitate further downstream processing, though results from each caller are also retained.
+The flow is capable of accommodating additional variant calling software or CNV callers. It is also prepared to process normal, tumor and several relapse samples.
 
 Besides variant calls, the workflow provides quality controls presented by [MultiQC][multiqc-link].
 
@@ -40,7 +48,10 @@ The CAW pipeline comes with documentation about the pipeline, found in the `doc/
 14. [More information about ASCAT](doc/ASCAT.md)
 15. [Folder structure](doc/FOLDER.md)
 
-For further information/help contact: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se or join the gitter chat: [gitter.im/SciLifeLab/CAW][gitter-link].
+## Contributions & Support
+
+- [Contributions guidelines](.github/CONTRIBUTING.md)
+For further information/help, don't hesitate to get in touch on [Gitter][gitter-link] or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se
 
 ## Authors
 
@@ -63,6 +74,7 @@ For further information/help contact: maxime.garcia@scilifelab.se, szilveszter.j
 
 [ascat-link]: https://github.com/Crick-CancerGenomics/ascat
 [caw-site-link]: http://opensource.scilifelab.se/projects/caw/
+[freebayes-link]: https://github.com/ekg/freebayes
 [gatk-link]: https://github.com/broadgsa/gatk-protected
 [gitter-badge]: https://badges.gitter.im/SciLifeLab/CAW.svg
 [gitter-link]: https://gitter.im/SciLifeLab/CAW
@@ -76,7 +88,7 @@ For further information/help contact: maxime.garcia@scilifelab.se, szilveszter.j
 [nextflow-link]: https://www.nextflow.io/
 [ngi-link]: https://ngisweden.scilifelab.se/
 [scilifelab-link]: https://www.scilifelab.se/
-[scilifelab-stockholm-link]: https://www.scilifelab.se/platforms/ngi/
+[scilifelab-stockholm-link]: https://www.scilifelab.se/facilities/ngi-stockholm/
 [strelka-link]: https://github.com/Illumina/strelka
 [travis-badge]: https://api.travis-ci.org/SciLifeLab/CAW.svg
 [travis-link]: https://travis-ci.org/SciLifeLab/CAW
diff --git a/buildContainers.nf b/buildContainers.nf
index 7ed7ca4a4e..4e55c761c5 100644
--- a/buildContainers.nf
+++ b/buildContainers.nf
@@ -36,18 +36,18 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.4'
+version = '1.2.5'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
 nf_required_version = '0.25.0'
 try {
-    if( ! nextflow.version.matches(">= $nf_required_version") ){
+    if( ! nextflow.version.matches(">= ${nf_required_version}") ){
         throw GroovyException('Nextflow version too old')
     }
 } catch (all) {
     log.error "====================================================\n" +
-              "  Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\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" +
               "============================================================"
@@ -55,14 +55,14 @@ try {
 
 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"
+if (!isAllowedParams(params)) exit 1, "params 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 = ''
+// containerPath is current Directory
+params.containerPath = "${baseDir}"
 // all containers to be build
 params.containers = 'all'
 // Docker will not be used
@@ -70,22 +70,26 @@ params.docker = false
 // Containers will not be pushed on DockerHub
 params.push = false
 // DockerHub repository is maxulysse
+// TODO Change to a SciLifeLab repository
 params.repository = 'maxulysse'
 // Singularity will not be used
 params.singularity = false
 
-verbose = params.verbose
+// Define containers to handle (build/push or pull)
 containersList = defineContainersList()
 containers = params.containers.split(',').collect {it.trim()}
 containers = containers == ['all'] ? containersList : containers
-docker = params.docker ? true : false
+
+// push only to DockerHub, so only when using Docker
 push = params.docker && params.push ? true : false
-repository = params.repository
+
+// by default the tag will be the current version
 tag = params.tag ? params.tag : version
-singularity = params.singularity ? true : false
-containerPath = params.singularity && params.containerPath ? params.containerPath : "."
 
-if (!docker && !singularity) exit 1, 'No builder choose, specify --docker or --singularity, see --help for more information'
+// to simplify verbose mode
+verbose = params.verbose
+
+if (!params.docker && !params.singularity) exit 1, 'No container technology choosed, specify --docker or --singularity, see --help for more information'
 
 if (!checkContainers(containers,containersList)) exit 1, 'Unknown container(s), see --help for more information'
 
@@ -101,68 +105,68 @@ dockerContainers = containers
 singularityContainers = containers
 
 process BuildDockerContainers {
-  tag {repository + "/" + container + ":" + tag}
+  tag {"${params.repository}/${container}:${tag}"}
 
   input:
     val container from dockerContainers
 
   output:
-    val container into dockerContainersBuilt
+    val container into containersBuilt
 
-  when: docker
+  when: params.docker
 
   script:
   """
-  docker build -t $repository/$container:$tag $baseDir/containers/$container/.
+  docker build -t ${params.repository}/${container}:${tag} ${baseDir}/containers/${container}/.
   """
 }
 
-if (verbose) dockerContainersBuilt = dockerContainersBuilt.view {
-  "Docker container: $repository/$it:$tag built."
+if (verbose) containersBuilt = containersBuilt.view {
+  "Docker container: ${params.repository}/${it}:${tag} built."
 }
 
 process PullSingularityContainers {
-  tag {repository + "/" + container + ":" + tag}
+  tag {"${params.repository}/${container}:${tag}"}
 
-  publishDir containerPath, mode: 'move'
+  publishDir "${params.containerPath}", mode: 'move'
 
   input:
     val container from singularityContainers
 
   output:
-    file("*.img") into singularityContainersPulled
+    file("${container}-${tag}.img") into imagePulled
 
-  when: singularity
+  when: params.singularity
 
   script:
   """
-  singularity pull --name $container-${tag}.img docker://$repository/$container:$tag
+  singularity pull --name ${container}-${tag}.img docker://${params.repository}/${container}:${tag}
   """
 }
 
-if (verbose) singularityContainersPulled = singularityContainersPulled.view {
-  "Singularity container: $it pulled."
+if (verbose) imagePulled = imagePulled.view {
+  "Singularity image: ${it.fileName} pulled."
 }
 
 process PushDockerContainers {
-  tag {repository + "/" + container + ":" + tag}
+  tag {params.repository + "/" + container + ":" + tag}
 
   input:
-    val container from dockerContainersBuilt
+    val container from containersBuilt
 
   output:
-    val container into dockerContainersPushed
+    val container into containersPushed
 
-  when: docker && push
+  when: params.docker && push
 
   script:
   """
-  docker push $repository/$container:$tag
+  docker push ${params.repository}/${container}:${tag}
   """
 }
 
-if (verbose) dockerContainersPushed = dockerContainersPushed.view {
-  "Docker container: $repository/$it:$tag pushed."
+if (verbose) containersPushed = containersPushed.view {
+  "Docker container: ${params.repository}/${it}:${tag} pushed."
 }
 
 /*
@@ -173,13 +177,13 @@ if (verbose) dockerContainersPushed = dockerContainersPushed.view {
 
 def cawMessage() {
   // Display CAW message
-  log.info "CANCER ANALYSIS WORKFLOW ~ $version - " + this.grabRevision() + (workflow.commitId ? " [$workflow.commitId]" : "")
+  log.info "CANCER ANALYSIS WORKFLOW ~ ${version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def checkContainerExistence(container, list) {
   try {assert list.contains(container)}
   catch (AssertionError ae) {
-    println("Unknown container: $container")
+    println("Unknown container: ${container}")
     return false
   }
   return true
@@ -210,6 +214,7 @@ def checkParams(it) {
     'containerPath',
     'containers',
     'docker',
+    'genome_base',
     'genome',
     'genomes',
     'help',
@@ -217,6 +222,9 @@ def checkParams(it) {
     'no-reports',
     'noGVCF',
     'noReports',
+    'out-dir',
+    'outDir',
+    'params',
     'project',
     'push',
     'repository',
@@ -273,12 +281,12 @@ def helpMessage() {
   // Display help message
   this.cawMessage()
   log.info "    Usage:"
-  log.info "       nextflow run SciLifeLab/buildContainers.nf [--docker] [--push]"
+  log.info "       nextflow run SciLifeLab/CAW/buildContainers.nf [--docker] [--push]"
   log.info "          [--containers <container1...>] [--singularity]"
   log.info "          [--containerPath <path>]"
   log.info "          [--tag <tag>] [--repository <repository>]"
   log.info "    Example:"
-  log.info "      nextflow run . --docker --containers multiqc,fastqc"
+  log.info "      nextflow run SciLifeLab/CAW/buildContainers.nf --docker --containers caw"
   log.info "    --containers: Choose which containers to build"
   log.info "       Default: all"
   log.info "       Possible values:"
@@ -291,10 +299,10 @@ def helpMessage() {
   log.info "    --push: Push containers to DockerHub"
   log.info "    --repository: Build containers under given repository"
   log.info "       Default: maxulysse"
-  log.info "    --singularity: Build containers using Singularity"
-  log.info "    --containerPath: Select where to download containers"
-  log.info "       Default: $PWD"
-  log.info "    --tag`: Build containers using given tag"
+  log.info "    --singularity: Download Singularity images"
+  log.info "    --containerPath: Select where to download images"
+  log.info "       Default: \$PWD"
+  log.info "    --tag`: Choose the tag for the containers"
   log.info "       Default (version number): " + version
   log.info "    --version"
   log.info "       displays version number and more informations"
@@ -314,16 +322,17 @@ def isAllowedParams(params) {
 
 def minimalInformationMessage() {
   // Minimal information message
-  log.info "Command Line: $workflow.commandLine"
-  log.info "Project Dir : $workflow.projectDir"
-  log.info "Launch Dir  : $workflow.launchDir"
-  log.info "Work Dir    : $workflow.workDir"
+  log.info "Command Line: " + workflow.commandLine
+  log.info "Project Dir : " + workflow.projectDir
+  log.info "Launch Dir  : " + workflow.launchDir
+  log.info "Work Dir    : " + workflow.workDir
+  log.info "Cont. Path  : " + params.containerPath
   log.info "Containers  : " + containers.join(', ')
 }
 
 def nextflowMessage() {
   // Nextflow message (version + build)
-  log.info "N E X T F L O W  ~  version $workflow.nextflow.version $workflow.nextflow.build"
+  log.info "N E X T F L O W  ~  version ${workflow.nextflow.version} ${workflow.nextflow.build}"
 }
 
 def startMessage() {
@@ -335,8 +344,8 @@ def startMessage() {
 def versionMessage() {
   // Display version message
   log.info "CANCER ANALYSIS WORKFLOW"
-  log.info "  version   : $version"
-  log.info workflow.commitId ? "Git info    : $workflow.repository - $workflow.revision [$workflow.commitId]" : "  revision  : " + this.grabRevision()
+  log.info "  version   : " + version
+  log.info workflow.commitId ? "Git info    : ${workflow.repository} - ${workflow.revision} [${workflow.commitId}]" : "  revision  : " + this.grabRevision()
 }
 
 workflow.onComplete {
@@ -344,10 +353,10 @@ workflow.onComplete {
   this.nextflowMessage()
   this.cawMessage()
   this.minimalInformationMessage()
-  log.info "Completed at: $workflow.complete"
-  log.info "Duration    : $workflow.duration"
-  log.info "Success     : $workflow.success"
-  log.info "Exit status : $workflow.exitStatus"
+  log.info "Completed at: " + workflow.complete
+  log.info "Duration    : " + workflow.duration
+  log.info "Success     : " + workflow.success
+  log.info "Exit status : " + workflow.exitStatus
   log.info "Error report: " + (workflow.errorReport ?: '-')
 }
 
@@ -355,5 +364,6 @@ workflow.onError {
   // Display error message
   this.nextflowMessage()
   this.cawMessage()
-  log.info "Workflow execution stopped with the following message: " + workflow.errorMessage
+  log.info "Workflow execution stopped with the following message:"
+  log.info "  " + workflow.errorMessage
 }
diff --git a/buildReferences.nf b/buildReferences.nf
index c3e52718eb..14a3e46be8 100644
--- a/buildReferences.nf
+++ b/buildReferences.nf
@@ -39,18 +39,18 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.4'
+version = '1.2.5'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
 nf_required_version = '0.25.0'
 try {
-    if( ! nextflow.version.matches(">= $nf_required_version") ){
+    if( ! nextflow.version.matches(">= ${nf_required_version}") ){
         throw GroovyException('Nextflow version too old')
     }
 } catch (all) {
     log.error "====================================================\n" +
-              "  Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\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" +
               "============================================================"
@@ -58,14 +58,16 @@ try {
 
 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"
+if (!isAllowedParams(params)) exit 1, "params 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
+// No download of reference source files
 params.download = false
+// outDir is References/${params.genome}
+params.outDir = "${baseDir}/References/${params.genome}"
 // refDir is empty
 params.refDir = ''
 
@@ -91,7 +93,7 @@ if (params.genome == "smallGRCh37") {
     [
       '1000G_phase1.indels.b37.vcf.gz',
       '1000G_phase3_20130502_SNP_maf0.3.loci.tar.bz2',
-      'b37_cosmic_v74.noCHR.sort.4.1.vcf.tar.bz2',
+      'GRCh37_Cosmic_v83.vcf.tar.bz2',
       'dbsnp_138.b37.vcf.gz',
       'human_g1k_v37_decoy.fasta.gz',
       'Mills_and_1000G_gold_standard.indels.b37.vcf.gz',
@@ -99,7 +101,7 @@ if (params.genome == "smallGRCh37") {
     ]
 } else exit 1, "Can't build this reference genome"
 
-if (download && params.genome != "smallGRCh37") exit 1, "Not possible to download $params.genome references files"
+if (download && params.genome != "smallGRCh37") exit 1, "Not possible to download ${params.genome} references files"
 
 if (!download) referencesFiles.each{checkFile(params.refDir + "/" + it)}
 
@@ -124,18 +126,18 @@ process ProcessReference {
 
   if (download)
   """
-  wget https://github.com/szilvajuhos/smallRef/raw/master/$reference
+  wget https://github.com/szilvajuhos/smallRef/raw/master/${reference}
   """
 
   else
   """
-  ln -s $params.refDir/$reference .
+  ln -s ${params.refDir}/${reference} .
   """
 }
 
 
 if (verbose) processedFiles = processedFiles.view {
-  "Files preprocessed  : $it.fileName"
+  "Files preprocessed  : ${it.fileName}"
 }
 
 compressedfiles = Channel.create()
@@ -154,19 +156,19 @@ process DecompressFile {
     file("*.{vcf,fasta,loci}") into decompressedFiles
 
   script:
-  realReference="readlink $reference"
+  realReference="readlink ${reference}"
   if (reference =~ ".gz")
     """
-    gzip -d -c \$($realReference) > $reference.baseName
+    gzip -d -c \$(${realReference}) > ${reference.baseName}
     """
   else if (reference =~ ".tar.bz2")
     """
-    tar xvjf \$($realReference)
+    tar xvjf \$(${realReference})
     """
 }
 
 if (verbose) decompressedFiles = decompressedFiles.view {
-  "Files decomprecessed: $it.fileName"
+  "Files decomprecessed: ${it.fileName}"
 }
 
 fastaFile = Channel.create()
@@ -180,7 +182,7 @@ decompressedFiles
 
 notCompressedfiles
   .mix(otherFiles)
-  .collectFile(storeDir: "References/" + params.genome)
+  .collectFile(storeDir: params.outDir)
 
 fastaForBWA = Channel.create()
 fastaForPicard = Channel.create()
@@ -191,7 +193,7 @@ fastaFile.into(fastaForBWA,fastaForPicard,fastaForSAMTools)
 process BuildBWAindexes {
   tag {reference}
 
-  publishDir "References/" + params.genome, mode: 'copy'
+  publishDir params.outDir, mode: 'copy'
 
   input:
     file(reference) from fastaForBWA
@@ -203,21 +205,21 @@ process BuildBWAindexes {
   script:
 
   """
-  bwa index $reference
+  bwa index ${reference}
   """
 }
 
 if (verbose) fastaFileToKeep.view {
-  "Fasta File          : $it.fileName"
+  "Fasta File          : ${it.fileName}"
 }
 if (verbose) bwaIndexes.flatten().view {
-  "BWA index           : $it.fileName"
+  "BWA index           : ${it.fileName}"
 }
 
 process BuildPicardIndex {
   tag {reference}
 
-  publishDir "References/" + params.genome, mode: 'copy'
+  publishDir params.outDir, mode: 'copy'
 
   input:
     file(reference) from fastaForPicard
@@ -230,19 +232,19 @@ process BuildPicardIndex {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$PICARD_HOME/picard.jar \
   CreateSequenceDictionary \
-  REFERENCE=$reference \
+  REFERENCE=${reference} \
   OUTPUT=${reference.baseName}.dict
   """
 }
 
 if (verbose) picardIndex.view {
-  "Picard index        : $it.fileName"
+  "Picard index        : ${it.fileName}"
 }
 
 process BuildSAMToolsIndex {
   tag {reference}
 
-  publishDir "References/" + params.genome, mode: 'copy'
+  publishDir params.outDir, mode: 'copy'
 
   input:
     file(reference) from fastaForSAMTools
@@ -252,18 +254,18 @@ process BuildSAMToolsIndex {
 
   script:
   """
-  samtools faidx $reference
+  samtools faidx ${reference}
   """
 }
 
 if (verbose) samtoolsIndex.view {
-  "SAMTools index      : $it.fileName"
+  "SAMTools index      : ${it.fileName}"
 }
 
 process BuildVCFIndex {
   tag {reference}
 
-  publishDir "References/" + params.genome, mode: 'copy'
+  publishDir params.outDir, mode: 'copy'
 
   input:
     file(reference) from vcfFiles
@@ -274,15 +276,15 @@ process BuildVCFIndex {
 
   script:
   """
-  \$IGVTOOLS_HOME/igvtools index $reference
+  \$IGVTOOLS_HOME/igvtools index ${reference}
   """
 }
 
 if (verbose) vcfIndexed.view {
-  "VCF indexed         : $it.fileName"
+  "VCF indexed         : ${it.fileName}"
 }
 if (verbose) vcfIndex.view {
-  "VCF index           : $it.fileName"
+  "VCF index           : ${it.fileName}"
 }
 
 /*
@@ -293,13 +295,13 @@ if (verbose) vcfIndex.view {
 
 def cawMessage() {
   // Display CAW message
-  log.info "CANCER ANALYSIS WORKFLOW ~ $version - " + this.grabRevision() + (workflow.commitId ? " [$workflow.commitId]" : "")
+  log.info "CANCER ANALYSIS WORKFLOW ~ ${version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def checkFile(it) {
   // Check file existence
   final f = file(it)
-  if (!f.exists()) exit 1, "Missing file: $it, see --help for more information"
+  if (!f.exists()) exit 1, "Missing file: ${it}, see --help for more information"
   return true
 }
 
@@ -320,6 +322,7 @@ def checkParams(it) {
     'containers',
     'docker',
     'download',
+    'genome_base',
     'genome',
     'genomes',
     'help',
@@ -327,6 +330,9 @@ def checkParams(it) {
     'no-reports',
     'noGVCF',
     'noReports',
+    'out-dir',
+    'outDir',
+    'params',
     'project',
     'push',
     'ref-dir',
@@ -372,11 +378,14 @@ def helpMessage() {
   log.info "       Download reference files. (only with --genome smallGRCh37)"
   log.info "    --refDir <Directoy>"
   log.info "       Specify a directory containing reference files."
+  log.info "    --outDir <Directoy>"
+  log.info "       Specify an output directory"
+  log.info "       Default: \$PWD/References/"
   log.info "    --genome <Genome>"
-  log.info "       Use a specific genome version."
+  log.info "       Choose which genome to build references from"
   log.info "       Possible values are:"
   log.info "         GRCh37"
-  log.info "         smallGRCh37 (Build a small reference (for tests))"
+  log.info "         smallGRCh37"
   log.info "    --help"
   log.info "       you're reading it"
   log.info "    --version"
@@ -397,16 +406,17 @@ def isAllowedParams(params) {
 
 def minimalInformationMessage() {
   // Minimal information message
-  log.info "Command Line: $workflow.commandLine"
-  log.info "Project Dir : $workflow.projectDir"
-  log.info "Launch Dir  : $workflow.launchDir"
-  log.info "Work Dir    : $workflow.workDir"
+  log.info "Command Line: " + workflow.commandLine
+  log.info "Project Dir : " + workflow.projectDir
+  log.info "Launch Dir  : " + workflow.launchDir
+  log.info "Work Dir    : " + workflow.workDir
+  log.info "Out Dir     : " + params.outDir
   log.info "Genome      : " + params.genome
 }
 
 def nextflowMessage() {
   // Nextflow message (version + build)
-  log.info "N E X T F L O W  ~  version $workflow.nextflow.version $workflow.nextflow.build"
+  log.info "N E X T F L O W  ~  version ${workflow.nextflow.version} ${workflow.nextflow.build}"
 }
 
 def startMessage() {
@@ -418,8 +428,8 @@ def startMessage() {
 def versionMessage() {
   // Display version message
   log.info "CANCER ANALYSIS WORKFLOW"
-  log.info "  version   : $version"
-  log.info workflow.commitId ? "Git info    : $workflow.repository - $workflow.revision [$workflow.commitId]" : "  revision  : " + this.grabRevision()
+  log.info "  version   : " + version
+  log.info workflow.commitId ? "Git info    : ${workflow.repository} - ${workflow.revision} [${workflow.commitId}]" : "  revision  : " + this.grabRevision()
 }
 
 workflow.onComplete {
@@ -427,10 +437,10 @@ workflow.onComplete {
   this.nextflowMessage()
   this.cawMessage()
   this.minimalInformationMessage()
-  log.info "Completed at: $workflow.complete"
-  log.info "Duration    : $workflow.duration"
-  log.info "Success     : $workflow.success"
-  log.info "Exit status : $workflow.exitStatus"
+  log.info "Completed at: " + workflow.complete
+  log.info "Duration    : " + workflow.duration
+  log.info "Success     : " + workflow.success
+  log.info "Exit status : " + workflow.exitStatus
   log.info "Error report: " + (workflow.errorReport ?: '-')
 }
 
@@ -438,5 +448,6 @@ workflow.onError {
   // Display error message
   this.nextflowMessage()
   this.cawMessage()
-  log.info "Workflow execution stopped with the following message: " + workflow.errorMessage
+  log.info "Workflow execution stopped with the following message:"
+  log.info "  " + workflow.errorMessage
 }
diff --git a/configuration/aws-batch.config b/configuration/aws-batch.config
new file mode 100644
index 0000000000..b91e10bf93
--- /dev/null
+++ b/configuration/aws-batch.config
@@ -0,0 +1,30 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ *  Nextflow config file for Amazon Web Services
+ * -------------------------------------------------
+ * Imported under the 'aws' Nextflow profile in nextflow.config
+ * Defines reference genomes, using paths from s3
+ * To be use with AWS Batch
+ */
+
+params {
+  genome_base = params.genome == 'GRCh37' ? "s3://caw-references/grch37" : params.genome == 'GRCh38' ? "s3://caw-references/grch38" : "s3://caw-references/smallgrch37"
+  repository='maxulysse'
+  tag='1.2.5'
+}
+
+executor.name = 'awsbatch'
+executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+
+process {
+  executor = 'awsbatch'
+  queue = 'caw-job-queue'
+
+  errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
+  maxErrors = '-1'
+  maxRetries = 2
+  cpus = 2
+  memory = 7.GB
+}
diff --git a/configuration/base.config b/configuration/base.config
new file mode 100644
index 0000000000..eba6dcedc0
--- /dev/null
+++ b/configuration/base.config
@@ -0,0 +1,17 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ * Nextflow config file for CAW project
+ * -------------------------------------------------
+ * Basic configuration for some process
+ * -------------------------------------------------
+ */
+
+process {
+  $ConcatVCF {
+    // For unknown reasons, ConcatVCF sometimes fails with SIGPIPE
+    // (exit code 141). Rerunning the process will usually work.
+    errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
+  }
+}
diff --git a/configuration/containers.config b/configuration/containers.config
index d8015cca13..b35c6d701b 100644
--- a/configuration/containers.config
+++ b/configuration/containers.config
@@ -10,6 +10,10 @@ vim: syntax=groovy
  */
 
 process {
+  // Add container for processes without containers
+  $CreateIntervalBeds.container       = "${params.repository}/caw:${params.tag}"
+  $GenerateMultiQCconfig.container    = "${params.repository}/caw:${params.tag}"
+
   $BuildBWAindexes.container          = "${params.repository}/caw:${params.tag}"
   $BuildPicardIndex.container         = "${params.repository}/picard:${params.tag}"
   $BuildSAMToolsIndex.container       = "${params.repository}/caw:${params.tag}"
@@ -38,7 +42,7 @@ process {
   $RunSamtoolsStats.container         = "${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}"}
+  $RunSnpeff.container = {params.genome == 'GRCh38' ? "${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}"}
+  $RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
 }
diff --git a/configuration/docker.config b/configuration/docker.config
index 69711042ad..876fc9c5a6 100644
--- a/configuration/docker.config
+++ b/configuration/docker.config
@@ -14,5 +14,7 @@ docker {
   fixOwnership = true
 }
 
-params.repository='maxulysse'
-params.tag='1.2.3'
+params {
+  repository='maxulysse'
+  tag='1.2.5'
+}
diff --git a/configuration/genomes.config b/configuration/genomes.config
index 406dec6fe0..f65ea98c30 100644
--- a/configuration/genomes.config
+++ b/configuration/genomes.config
@@ -16,51 +16,48 @@ vim: syntax=groovy
 params {
   genomes {
     'GRCh37' {
-      bundleDir   = '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37'
-      acLoci      = "$bundleDir/1000G_phase3_20130502_SNP_maf0.3.loci"
-      cosmic      = "$bundleDir/GRCh37_Cosmic_v83.vcf"
+      acLoci      = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.loci"
+      cosmic      = "${params.genome_base}/GRCh37_Cosmic_v83.vcf"
       cosmicIndex = "${cosmic}.idx"
-      dbsnp       = "$bundleDir/dbsnp_138.b37.vcf"
+      dbsnp       = "${params.genome_base}/dbsnp_138.b37.vcf"
       dbsnpIndex  = "${dbsnp}.idx"
-      genomeFile  = "$bundleDir/human_g1k_v37_decoy.fasta"
+      genomeFile  = "${params.genome_base}/human_g1k_v37_decoy.fasta"
       bwaIndex    = "${genomeFile}.{amb,ann,bwt,pac,sa}"
-      genomeDict  = "$bundleDir/human_g1k_v37_decoy.dict"
+      genomeDict  = "${params.genome_base}/human_g1k_v37_decoy.dict"
       genomeIndex = "${genomeFile}.fai"
-      intervals   = "$bundleDir/wgs_calling_regions_CAW.list"
-      knownIndels = "$bundleDir/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
-      knownIndelsIndex = "$bundleDir/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
+      intervals   = "${params.genome_base}/wgs_calling_regions_CAW.list"
+      knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
+      knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
       snpeffDb    = "GRCh37.75"
     }
     'GRCh38' {
-      bundleDir     = '/sw/data/uppnex/ToolBox/hg38bundle'
-      acLoci        = "${bundleDir}/1000G_phase3_GRCh38_maf0.3.loci"
-      cosmic        = "${bundleDir}/COSMICv80.vcf"
+      acLoci        = "${params.genome_base}/1000G_phase3_GRCh38_maf0.3.loci"
+      cosmic        = "${params.genome_base}/COSMICv80.vcf"
       cosmicIndex   = "${cosmic}.idx"
-      dbsnp         = "$bundleDir/dbsnp_146.hg38.vcf.gz"
+      dbsnp         = "${params.genome_base}/dbsnp_146.hg38.vcf.gz"
       dbsnpIndex    = "${dbsnp}.tbi"
-      genomeFile    = "$bundleDir/Homo_sapiens_assembly38.fasta"
-      genomeDict    = "$bundleDir/Homo_sapiens_assembly38.dict"
+      genomeFile    = "${params.genome_base}/Homo_sapiens_assembly38.fasta"
+      genomeDict    = "${params.genome_base}/Homo_sapiens_assembly38.dict"
       genomeIndex   = "${genomeFile}.fai"
       bwaIndex      = "${genomeFile}.64.{amb,ann,bwt,pac,sa,alt}"
-      intervals     = "$bundleDir/wgs_calling_regions.hg38.bed"
-      knownIndels   = "$bundleDir/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
-      knownIndelsIndex = "$bundleDir/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
+      intervals     = "${params.genome_base}/wgs_calling_regions.hg38.bed"
+      knownIndels   = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
+      knownIndelsIndex = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
       snpeffDb      = "GRCh38.86"
     }
     'smallGRCh37' {
-      bundleDir   = 'References/smallGRCh37'
-      acLoci      = "$bundleDir/1000G_phase3_20130502_SNP_maf0.3.small.loci"
-      cosmic      = "$bundleDir/b37_cosmic_v74.noCHR.sort.4.1.small.vcf"
+      acLoci      = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
+      cosmic      = "${params.genome_base}/b37_cosmic_v74.noCHR.sort.4.1.small.vcf"
       cosmicIndex = "${cosmic}.idx"
-      dbsnp       = "$bundleDir/dbsnp_138.b37.small.vcf"
+      dbsnp       = "${params.genome_base}/dbsnp_138.b37.small.vcf"
       dbsnpIndex  = "${dbsnp}.idx"
-      genomeFile  = "$bundleDir/human_g1k_v37_decoy.small.fasta"
+      genomeFile  = "${params.genome_base}/human_g1k_v37_decoy.small.fasta"
       bwaIndex    = "${genomeFile}.{amb,ann,bwt,pac,sa}"
-      genomeDict  = "$bundleDir/human_g1k_v37_decoy.small.dict"
+      genomeDict  = "${params.genome_base}/human_g1k_v37_decoy.small.dict"
       genomeIndex = "${genomeFile}.fai"
-      intervals   = "$bundleDir/small.intervals"
-      knownIndels = "$bundleDir/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf"
-      knownIndelsIndex = "$bundleDir/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx"
+      intervals   = "${params.genome_base}/small.intervals"
+      knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf"
+      knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx"
       snpeffDb    = "GRCh37.75"
     }
   }
diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
index 8ce9cb3d93..b96b78edf8 100644
--- a/configuration/singularity-path.config
+++ b/configuration/singularity-path.config
@@ -15,8 +15,10 @@ singularity {
   runOptions = "--bind /scratch"
 }
 
-params.containerPath='containers'
-params.tag='1.2.3'
+params {
+  containerPath='containers'
+  tag='1.2.5'
+}
 
 process {
   $BuildBWAindexes.container          = "${params.containerPath}/caw-${params.tag}.img"
@@ -48,7 +50,7 @@ process {
   $RunSamtoolsStats.container         = "${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"}
+  $RunSnpeff.container                = {params.genome == 'GRCh38' ? "${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"}
+  $RunVEP.container                   = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
 }
diff --git a/configuration/singularity.config b/configuration/singularity.config
index 198b45a9e2..429cf47b0b 100644
--- a/configuration/singularity.config
+++ b/configuration/singularity.config
@@ -13,5 +13,7 @@ singularity {
   enabled = true
 }
 
-params.repository='docker://maxulysse'
-params.tag='1.2.3'
+params {
+  repository='docker://maxulysse'
+  tag='1.2.5'
+}
diff --git a/configuration/travis.config b/configuration/travis.config
index 4247856093..010669bc1b 100644
--- a/configuration/travis.config
+++ b/configuration/travis.config
@@ -11,6 +11,7 @@ vim: syntax=groovy
 
 params {
   genome = 'smallGRCh37'
+  genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
 }
 
 process {
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
index ba91dc2508..0ef861d959 100644
--- a/configuration/uppmax-localhost.config
+++ b/configuration/uppmax-localhost.config
@@ -14,6 +14,7 @@ env {
 }
 
 params {
+  genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
   singleCPUMem  = 8.GB
   totalMemory = 104.GB // change to 240 on irma
 }
@@ -58,9 +59,6 @@ process {
 
   $ConcatVCF {
     cpus = 8
-    // For unknown reasons, ConcatVCF sometimes fails with SIGPIPE
-    // (exit code 141). Rerunning the process will usually work.
-    errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
   }
   $CreateRecalibrationTable {
     cpus = 16
diff --git a/configuration/uppmax-slurm.config b/configuration/uppmax-slurm.config
index 38549cc48b..ae38a5866c 100644
--- a/configuration/uppmax-slurm.config
+++ b/configuration/uppmax-slurm.config
@@ -9,6 +9,7 @@ vim: syntax=groovy
  */
 
 params {
+  genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
   runTime       = 48.h
   singleCPUMem  = 7.GB // for processes that are using more memory but a single CPU only. Use the 'core' queue for these
 }
diff --git a/containers/multiqc/Dockerfile b/containers/multiqc/Dockerfile
index 42f7e99e15..8b5cf6541d 100644
--- a/containers/multiqc/Dockerfile
+++ b/containers/multiqc/Dockerfile
@@ -1,12 +1,9 @@
-FROM python:2.7-slim
+FROM ewels/multiqc:v1.3
 
 LABEL \
   author="Maxime Garcia" \
   description="MultiQC image used in CAW" \
   maintainer="maxime.garcia@scilifelab.se"
 
-# Build container
-ADD \
-  build.sh /usr/bin/
-RUN \
-  build.sh
+# Create UPPMAX directories
+RUN mkdir /pica /proj /scratch /sw
diff --git a/containers/multiqc/build.sh b/containers/multiqc/build.sh
deleted file mode 100755
index 4c6bf899d6..0000000000
--- a/containers/multiqc/build.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/sh
-set -eu pipefail
-
-# Local ENV variables
-MULTIQC_VERSION=1.1
-
-# Install libraries
-apt-get update && apt-get install -y --no-install-recommends \
-  g++ \
-  git \
-  wget
-
-# Install pip
-wget --quiet -O /opt/get-pip.py https://bootstrap.pypa.io/get-pip.py
-python /opt/get-pip.py
-
-# Install tools
-pip install networkx==1.11 # fix issue 592
-pip install git+git://github.com/ewels/MultiQC.git@v${MULTIQC_VERSION}
-
-# Clean up install
-cd /
-apt-get remove -y \
-  g++ \
-  git \
-  wget
-rm -rf /build /var/lib/apt/lists/* /opt/get-pip.py
-
-# Create UPPMAX directories
-mkdir /pica /proj /scratch /sw
diff --git a/containers/mutect1/Dockerfile b/containers/mutect1/Dockerfile
index 7c0d2a3f6e..1e2c72e1fa 100644
--- a/containers/mutect1/Dockerfile
+++ b/containers/mutect1/Dockerfile
@@ -23,5 +23,6 @@ RUN \
   && unzip muTect-${MUTECT_VERSION}-bin.zip -d ${MUTECT_HOME} \
   && rm muTect-${MUTECT_VERSION}-bin.zip \
 && mv ${MUTECT_HOME}/muTect-${MUTECT_VERSION}.jar ${MUTECT_HOME}/muTect.jar
+
 # Create UPPMAX directories
 RUN mkdir /pica /proj /scratch /sw
diff --git a/data/tiny/dummy_normal_reads_1.fastq.gz b/data/tiny/dummy/normal/dummy_n_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/dummy_normal_reads_1.fastq.gz
rename to data/tiny/dummy/normal/dummy_n_R1_xxx.fastq.gz
diff --git a/data/tiny/dummy_normal_reads_2.fastq.gz b/data/tiny/dummy/normal/dummy_n_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/dummy_normal_reads_2.fastq.gz
rename to data/tiny/dummy/normal/dummy_n_R2_xxx.fastq.gz
diff --git a/data/tiny/dummy_tumour_reads_1.fastq.gz b/data/tiny/dummy/tumor/dummy_t_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/dummy_tumour_reads_1.fastq.gz
rename to data/tiny/dummy/tumor/dummy_t_R1_xxx.fastq.gz
diff --git a/data/tiny/dummy_tumour_reads_2.fastq.gz b/data/tiny/dummy/tumor/dummy_t_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/dummy_tumour_reads_2.fastq.gz
rename to data/tiny/dummy/tumor/dummy_t_R2_xxx.fastq.gz
diff --git a/data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_1.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_1.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz
diff --git a/data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_2.fastq.gz b/data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_2.fastq.gz
rename to data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_1.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_1.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_2.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_2.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_1.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_1.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_2.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_2.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_1.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_1.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_2.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_2.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_1.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_1.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_2.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_2.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_1.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_1.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz
diff --git a/data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_2.fastq.gz b/data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_2.fastq.gz
rename to data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L001_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L001_R1_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L001_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L001_R2_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L002_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L002_R1_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L002_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L002_R2_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L004_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L004_R1_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L004_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L004_R2_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L007_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L007_R1_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L007_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L007_R2_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L008_R1_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L008_R1_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny/normal/tiny_normal_L008_R2_TEST.fastq.gz b/data/tiny/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny/normal/tiny_normal_L008_R2_TEST.fastq.gz
rename to data/tiny/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L001_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L001_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L001_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L001_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L002_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L002_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L002_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L002_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L003_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L003_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L003_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L003_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L005_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L005_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L005_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L005_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L006_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L006_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L006_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L006_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L007_R1.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L007_R1.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz
diff --git a/data/tiny/tiny_tumor_L007_R2.fastq.gz b/data/tiny/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz
similarity index 100%
rename from data/tiny/tiny_tumor_L007_R2.fastq.gz
rename to data/tiny/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz
diff --git a/data/tiny/tiny_normal_L001_R1.fastq.gz b/data/tiny/tiny_normal_L001_R1.fastq.gz
deleted file mode 100644
index b25487aa91..0000000000
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diff --git a/data/tiny/tiny_normal_L001_R2.fastq.gz b/data/tiny/tiny_normal_L001_R2.fastq.gz
deleted file mode 100644
index b917c80cef..0000000000
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diff --git a/data/tiny/tiny_normal_L002_R1.fastq.gz b/data/tiny/tiny_normal_L002_R1.fastq.gz
deleted file mode 100644
index 509295fdf7..0000000000
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diff --git a/data/tiny/tiny_normal_L002_R2.fastq.gz b/data/tiny/tiny_normal_L002_R2.fastq.gz
deleted file mode 100644
index ae0e1e6ee7..0000000000
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diff --git a/data/tiny/tiny_normal_L004_R1.fastq.gz b/data/tiny/tiny_normal_L004_R1.fastq.gz
deleted file mode 100644
index 29e4a3bd15..0000000000
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diff --git a/data/tiny/tiny_normal_L004_R2.fastq.gz b/data/tiny/tiny_normal_L004_R2.fastq.gz
deleted file mode 100644
index f645870a8f..0000000000
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diff --git a/data/tiny/tiny_normal_L007_R1.fastq.gz b/data/tiny/tiny_normal_L007_R1.fastq.gz
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index 8e3c3d295a..0000000000
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diff --git a/data/tiny/tiny_normal_L007_R2.fastq.gz b/data/tiny/tiny_normal_L007_R2.fastq.gz
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index ec28edfb5d..0000000000
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index f02dc49a05..0000000000
Binary files a/data/tiny/tiny_normal_L008_R2.fastq.gz and /dev/null differ
diff --git a/data/tsv/tiny-manta-s3.tsv b/data/tsv/tiny-manta-s3.tsv
new file mode 100644
index 0000000000..60ded74015
--- /dev/null
+++ b/data/tsv/tiny-manta-s3.tsv
@@ -0,0 +1,11 @@
+1234	XX	0	1234N	1234N_M1	s3://caw-test-data/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M2	s3://caw-test-data/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M4	s3://caw-test-data/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M5	s3://caw-test-data/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M6	s3://caw-test-data/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M7	s3://caw-test-data/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz	s3://caw-test-data/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M1	s3://caw-test-data/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz	s3://caw-test-data/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M2	s3://caw-test-data/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz	s3://caw-test-data/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M3	s3://caw-test-data/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz	s3://caw-test-data/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M4	s3://caw-test-data/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz	s3://caw-test-data/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M5	s3://caw-test-data/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz	s3://caw-test-data/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tsv/tiny-manta.tsv b/data/tsv/tiny-manta.tsv
index 33a74ea431..2c354fa968 100644
--- a/data/tsv/tiny-manta.tsv
+++ b/data/tsv/tiny-manta.tsv
@@ -1,11 +1,11 @@
-1234	XX	0	1234N	1234N_M1	data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_1.fastq.gz	data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M2	data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_1.fastq.gz	data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M4	data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_1.fastq.gz	data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M5	data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M6	data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M7	data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_2.fastq.gz
-1234	XX	1	9876T	9876T_M1	data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_1.fastq.gz	data/tiny/C09D_MANTA_TUMOUR_111207.3.ACCAACTG_2.fastq.gz
-1234	XX	1	9876T	9876T_M2	data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_1.fastq.gz	data/tiny/C09D_MANTA_TUMOUR_111207.5.ACCAACTG_2.fastq.gz
-1234	XX	1	9876T	9876T_M3	data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_1.fastq.gz	data/tiny/C09D_MANTA_TUMOUR_111207.6.ACCAACTG_2.fastq.gz
-1234	XX	1	9876T	9876T_M4	data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_1.fastq.gz	data/tiny/C09D_MANTA_TUMOUR_111207.7.ACCAACTG_2.fastq.gz
-1234	XX	1	9876T	9876T_M5	data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_1.fastq.gz	data/tiny/C09D_MANTA_TUMOUR_111207.8.ACCAACTG_2.fastq.gz
+1234	XX	0	1234N	1234N_M1	data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M2	data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M4	data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M5	data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M6	data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_M7	data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz	data/tiny/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M1	data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz	data/tiny/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M2	data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz	data/tiny/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M3	data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz	data/tiny/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M4	data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz	data/tiny/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_M5	data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz	data/tiny/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
diff --git a/data/tsv/tiny-s3.tsv b/data/tsv/tiny-s3.tsv
new file mode 100644
index 0000000000..e9270bb5a9
--- /dev/null
+++ b/data/tsv/tiny-s3.tsv
@@ -0,0 +1,13 @@
+1234	XX	0	1234N	1234N_1	s3://caw-test-data/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz	s3://caw-test-data/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_2	s3://caw-test-data/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz	s3://caw-test-data/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_4	s3://caw-test-data/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz	s3://caw-test-data/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_7	s3://caw-test-data/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz	s3://caw-test-data/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_8	s3://caw-test-data/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz	s3://caw-test-data/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
+1234	XX	0	1234N	DUMMY_N	s3://caw-test-data/dummy/normal/dummy_n_R1_xxx.fastq.gz	s3://caw-test-data/dummy/normal/dummy_n_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_1	s3://caw-test-data/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_2	s3://caw-test-data/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_3	s3://caw-test-data/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
+1234	XX	1	9876T	DUMMY_T	s3://caw-test-data/dummy/tumor/dummy_t_R1_xxx.fastq.gz	s3://caw-test-data/dummy/tumor/dummy_t_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_5	s3://caw-test-data/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_6	s3://caw-test-data/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_7	s3://caw-test-data/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz	s3://caw-test-data/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz
diff --git a/data/tsv/tiny-single-manta.tsv b/data/tsv/tiny-single-manta.tsv
deleted file mode 100644
index 29a7b5f137..0000000000
--- a/data/tsv/tiny-single-manta.tsv
+++ /dev/null
@@ -1,6 +0,0 @@
-1234	XX	0	1234N	1234N_M1	data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_1.fastq.gz	data/tiny/C097F_MANTA_NORMAL_111207.1.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M2	data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_1.fastq.gz	data/tiny/C097F_MANTA_NORMAL_111207.2.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M4	data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_1.fastq.gz	data/tiny/C09DF_MANTA_NORMAL_111207.4.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M5	data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.1.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M6	data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.2.AGTTGCTT_2.fastq.gz
-1234	XX	0	1234N	1234N_M7	data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_1.fastq.gz	data/tiny/D0F23_MANTA_NORMAL_111212.3.AGTTGCTT_2.fastq.gz
diff --git a/data/tsv/tiny.tsv b/data/tsv/tiny.tsv
index 09301edb08..d122b64562 100644
--- a/data/tsv/tiny.tsv
+++ b/data/tsv/tiny.tsv
@@ -1,19 +1,13 @@
-1234	XX	0	1234N	1234N_1	data/tiny/tiny_normal_L001_R1.fastq.gz	data/tiny/tiny_normal_L001_R2.fastq.gz
-1234	XX	0	1234N	1234N_2	data/tiny/tiny_normal_L002_R1.fastq.gz	data/tiny/tiny_normal_L002_R2.fastq.gz
-1234	XX	0	1234N	1234N_4	data/tiny/tiny_normal_L004_R1.fastq.gz	data/tiny/tiny_normal_L004_R2.fastq.gz
-1234	XX	0	1234N	1234N_7	data/tiny/tiny_normal_L007_R1.fastq.gz	data/tiny/tiny_normal_L007_R2.fastq.gz
-1234	XX	0	1234N	1234N_8	data/tiny/tiny_normal_L008_R1.fastq.gz	data/tiny/tiny_normal_L008_R2.fastq.gz
-1234	XX	0	1234N	DUMMY_N	data/tiny/dummy_normal_reads_1.fastq.gz	data/tiny/dummy_normal_reads_1.fastq.gz
-1234	XX	1	9876T	9876T_1	data/tiny/tiny_tumor_L001_R1.fastq.gz	data/tiny/tiny_tumor_L001_R2.fastq.gz
-1234	XX	1	9876T	9876T_2	data/tiny/tiny_tumor_L002_R1.fastq.gz	data/tiny/tiny_tumor_L002_R2.fastq.gz
-1234	XX	1	9876T	9876T_3	data/tiny/tiny_tumor_L003_R1.fastq.gz	data/tiny/tiny_tumor_L003_R2.fastq.gz
-1234	XX	1	9876T	9876T_5	data/tiny/tiny_tumor_L005_R1.fastq.gz	data/tiny/tiny_tumor_L005_R2.fastq.gz
-1234	XX	1	9876T	9876T_6	data/tiny/tiny_tumor_L006_R1.fastq.gz	data/tiny/tiny_tumor_L006_R2.fastq.gz
-1234	XX	1	9876T	9876T_7	data/tiny/tiny_tumor_L007_R1.fastq.gz	data/tiny/tiny_tumor_L007_R2.fastq.gz
-1234	XX	1	9876T	DUMMY_T	data/tiny/dummy_tumour_reads_1.fastq.gz	data/tiny/dummy_tumour_reads_1.fastq.gz
-1234	XX	1	9877R	9877R_1	data/tiny/tiny_tumor_L001_R1.fastq.gz	data/tiny/tiny_tumor_L001_R2.fastq.gz
-1234	XX	1	9877R	9877R_2	data/tiny/tiny_tumor_L002_R1.fastq.gz	data/tiny/tiny_tumor_L002_R2.fastq.gz
-1234	XX	1	9877R	9877R_3	data/tiny/tiny_tumor_L003_R1.fastq.gz	data/tiny/tiny_tumor_L003_R2.fastq.gz
-1234	XX	1	9877R	9877R_5	data/tiny/tiny_tumor_L005_R1.fastq.gz	data/tiny/tiny_tumor_L005_R2.fastq.gz
-1234	XX	1	9877R	9877R_6	data/tiny/tiny_tumor_L006_R1.fastq.gz	data/tiny/tiny_tumor_L006_R2.fastq.gz
-1234	XX	1	9877R	9877R_7	data/tiny/tiny_tumor_L007_R1.fastq.gz	data/tiny/tiny_tumor_L007_R2.fastq.gz
+1234	XX	0	1234N	1234N_1	data/tiny/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz	data/tiny/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_2	data/tiny/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz	data/tiny/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_4	data/tiny/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz	data/tiny/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_7	data/tiny/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz	data/tiny/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
+1234	XX	0	1234N	1234N_8	data/tiny/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz	data/tiny/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
+1234	XX	0	1234N	DUMMY_N	data/tiny/dummy/normal/dummy_n_R1_xxx.fastq.gz	data/tiny/dummy/normal/dummy_n_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_1	data/tiny/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_2	data/tiny/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
+1234	XX	1	9876T	9876T_3	data/tiny/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
+1234	XX	1	9876T	DUMMY_T	data/tiny/dummy/tumor/dummy_t_R1_xxx.fastq.gz	data/tiny/dummy/tumor/dummy_t_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_5	data/tiny/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_6	data/tiny/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
+1234	XX	1	9877R	9877R_7	data/tiny/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz	data/tiny/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz
diff --git a/doc/CONTAINERS.md b/doc/CONTAINERS.md
index ff7943f63c..aacd91d0f2 100644
--- a/doc/CONTAINERS.md
+++ b/doc/CONTAINERS.md
@@ -58,8 +58,8 @@ A container named after the process is made for each process. If a container can
 
 ## multiqc [![multiqc-docker status][multiqc-docker-badge]][multiqc-docker-link]
 
-- Based on `python:2.7-slim`
-- Contain **[MultiQC][multiqc-link]** 1.1
+- Based on `ewels/multiqc:v1.3`
+- Contain **[MultiQC][multiqc-link]** 1.3
 
 ## mutect1 [![mutect1-docker status][mutect1-docker-badge]][mutect1-docker-link]
 
diff --git a/doc/USAGE.md b/doc/USAGE.md
index 316693ec04..64f281ac8e 100644
--- a/doc/USAGE.md
+++ b/doc/USAGE.md
@@ -26,6 +26,10 @@ Display help
 
 Disable QC tools and MultiQC to generate a HTML report.
 
+### --outDir
+
+Choose an output directory
+
 ### --project `ProjectID`
 
 Specify a project number ID on a UPPMAX cluster. (optionnal if not on such a cluster)
diff --git a/main.nf b/main.nf
index 079f8890b2..16718090c5 100644
--- a/main.nf
+++ b/main.nf
@@ -62,23 +62,28 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.4'
+version = '1.2.5'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
 nf_required_version = '0.25.0'
 try {
-    if( ! nextflow.version.matches(">= $nf_required_version") ){
+    if( ! nextflow.version.matches(">= ${nf_required_version}") ){
         throw GroovyException('Nextflow version too old')
     }
 } catch (all) {
-    log.error "============================================================\n" +
-              "  Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\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" +
               "============================================================"
 }
 
+if (params.help) exit 0, helpMessage()
+if (params.version) exit 0, versionMessage()
+if (!isAllowedParams(params)) exit 1, "params 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
 
@@ -94,6 +99,10 @@ params.contactMail = ''
 params.noGVCF = false
 // Reports are generated
 params.noReports = false
+// BAMQC is used
+params.noBAMQC = false
+// outDir is current directory
+params.outDir = baseDir
 // No sample is defined
 params.sample = ''
 // No sampleDir is defined
@@ -104,11 +113,10 @@ params.step = 'mapping'
 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"
-if (!checkUppmaxProject()) exit 1, "No UPPMAX project ID found! Use --project <UPPMAX Project ID>"
+// Params are defined in config files
+params.containerPath = ''
+params.repository = ''
+params.tag = ''
 
 step = params.step.toLowerCase()
 if (step == 'preprocessing') step = 'mapping'
@@ -152,10 +160,10 @@ if (params.sample) tsvPath = params.sample
 // No need for tsv file for step annotate
 if (!params.sample && !params.sampleDir) {
   tsvPaths = [
-  'mapping': "$workflow.projectDir/data/tsv/tiny.tsv",
-  'realign': "$workflow.launchDir/$directoryMap.nonRealigned/nonRealigned.tsv",
-  'recalibrate': "$workflow.launchDir/$directoryMap.nonRecalibrated/nonRecalibrated.tsv",
-  'variantcalling': "$workflow.launchDir/$directoryMap.recalibrated/recalibrated.tsv"
+  'mapping': "${workflow.projectDir}/data/tsv/tiny.tsv",
+  'realign': "${params.outDir}/${directoryMap.nonRealigned}/nonRealigned.tsv",
+  'recalibrate': "${params.outDir}/${directoryMap.nonRecalibrated}/nonRecalibrated.tsv",
+  'variantcalling': "${params.outDir}/${directoryMap.recalibrated}/recalibrated.tsv"
   ]
   if (params.test || step != 'mapping') tsvPath = tsvPaths[step]
 }
@@ -171,7 +179,7 @@ if (tsvPath) {
     case 'realign': bamFiles = extractBams(tsvFile); break
     case 'recalibrate': bamFiles = extractRecal(tsvFile); break
     case 'variantcalling': bamFiles = extractBams(tsvFile); break
-    default: exit 1, "Unknown step $step"
+    default: exit 1, "Unknown step ${step}"
   }
 } else if (params.sampleDir) {
   if (step != 'mapping') exit 1, '--sampleDir does not support steps other than "mapping"'
@@ -185,11 +193,8 @@ if (tsvPath) {
   tsvFile = params.sampleDir  // used in the reports
 } else if (step != 'annotate') exit 1, 'No sample were defined, see --help'
 
-if (step == 'mapping') {
-  (patientGenders, fastqFiles) = extractGenders(fastqFiles)
-} else {
-  (patientGenders, bamFiles) = extractGenders(bamFiles)
-}
+if (step == 'mapping') (patientGenders, fastqFiles) = extractGenders(fastqFiles)
+else (patientGenders, bamFiles) = extractGenders(bamFiles)
 
 /*
 ================================================================================
@@ -216,7 +221,7 @@ if (verbose) bamFiles = bamFiles.view {
 process RunFastQC {
   tag {idPatient + "-" + idRun}
 
-  publishDir "$directoryMap.fastQC/$idRun", mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.fastQC}/${idRun}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, idRun, file(fastqFile1), file(fastqFile2) from fastqFilesforFastQC
@@ -228,7 +233,7 @@ process RunFastQC {
 
   script:
   """
-  fastqc -q $fastqFile1 $fastqFile2
+  fastqc -q ${fastqFile1} ${fastqFile2}
   """
 }
 
@@ -250,13 +255,13 @@ process MapReads {
   when: step == 'mapping'
 
   script:
-  readGroup = "@RG\\tID:$idRun\\tPU:$idRun\\tSM:$idSample\\tLB:$idSample\\tPL:illumina"
+  readGroup = "@RG\\tID:${idRun}\\tPU:${idRun}\\tSM:${idSample}\\tLB:${idSample}\\tPL:illumina"
   // adjust mismatch penalty for tumor samples
   extra = status == 1 ? "-B 3 " : ""
   """
-  bwa mem -R \"$readGroup\" ${extra}-t $task.cpus -M \
-  $genomeFile $fastqFile1 $fastqFile2 | \
-  samtools sort --threads $task.cpus -m 4G - > ${idRun}.bam
+  bwa mem -R \"${readGroup}\" ${extra}-t ${task.cpus} -M \
+  ${genomeFile} ${fastqFile1} ${fastqFile2} | \
+  samtools sort --threads ${task.cpus} -m 4G - > ${idRun}.bam
   """
 }
 
@@ -291,7 +296,7 @@ process MergeBams {
 
   script:
   """
-  samtools merge --threads $task.cpus ${idSample}.bam $bam
+  samtools merge --threads ${task.cpus} ${idSample}.bam ${bam}
   """
 }
 
@@ -318,7 +323,7 @@ if (verbose) mergedBam = mergedBam.view {
 process MarkDuplicates {
   tag {idPatient + "-" + idSample}
 
-  publishDir '.', saveAs: { it == "${bam}.metrics" ? "$directoryMap.markDuplicatesQC/$it" : "$directoryMap.nonRealigned/$it" }, mode: 'copy'
+  publishDir params.outDir, saveAs: { it == "${bam}.metrics" ? "${directoryMap.markDuplicatesQC}/${it}" : "${directoryMap.nonRealigned}/${it}" }, mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam) from mergedBam
@@ -347,23 +352,20 @@ process MarkDuplicates {
 // Creating a TSV file to restart from this step
 markDuplicatesTSV.map { idPatient, status, idSample, bam, bai ->
   gender = patientGenders[idPatient]
-  "$idPatient\t$gender\t$status\t$idSample\t$directoryMap.nonRealigned/$bam\t$directoryMap.nonRealigned/$bai\n"
+  "${idPatient}\t${gender}\t${status}\t${idSample}\t${params.outDir}/${directoryMap.nonRealigned}/${bam}\t${params.outDir}/${directoryMap.nonRealigned}/${bai}\n"
 }.collectFile(
-  name: 'nonRealigned.tsv', sort: true, storeDir: directoryMap.nonRealigned
+  name: 'nonRealigned.tsv', sort: true, storeDir: "${params.outDir}/${directoryMap.nonRealigned}"
 )
 
 // Create intervals for realignement using both tumor+normal as input
 // Group the marked duplicates BAMs for intervals and realign by idPatient
 // Grouping also by gender, to make a nicer channel
 duplicatesGrouped = Channel.empty()
-if (step == 'mapping') {
-  duplicatesGrouped = duplicates.groupTuple()
-} else if (step == 'realign') {
-  duplicatesGrouped = bamFiles.map{
-    idPatient, status, idSample, bam, bai ->
-    [idPatient, bam, bai]
-  }.groupTuple()
-}
+if (step == 'mapping') duplicatesGrouped = duplicates.groupTuple()
+else if (step == 'realign') duplicatesGrouped = bamFiles.map{
+  idPatient, status, idSample, bam, bai ->
+  [idPatient, bam, bai]
+}.groupTuple()
 
 // The duplicatesGrouped channel is duplicated
 // one copy goes to the RealignerTargetCreator process
@@ -386,7 +388,7 @@ if (verbose) duplicatesRealign = duplicatesRealign.view {
 
 if (verbose) markDuplicatesReport = markDuplicatesReport.view {
   "MarkDuplicates report:\n\
-  File  : [$it.fileName]"
+  File  : [${it.fileName}]"
 }
 
 // VCF indexes are added so they will be linked, and not re-created on the fly
@@ -412,17 +414,17 @@ process RealignerTargetCreator {
   when: step == 'mapping' || step == 'realign'
 
   script:
-  bams = bam.collect{"-I $it"}.join(' ')
-  known = knownIndels.collect{"-known $it"}.join(' ')
+  bams = bam.collect{"-I ${it}"}.join(' ')
+  known = knownIndels.collect{"-known ${it}"}.join(' ')
   """
   java -Xmx${task.memory.toGiga()}g \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T RealignerTargetCreator \
-  $bams \
-  -R $genomeFile \
-  $known \
-  -nt $task.cpus \
-  -L $intervals \
+  ${bams} \
+  -R ${genomeFile} \
+  ${known} \
+  -nt ${task.cpus} \
+  -L ${intervals} \
   -o ${idPatient}.intervals
   """
 }
@@ -470,16 +472,16 @@ process IndelRealigner {
   when: step == 'mapping' || step == 'realign'
 
   script:
-  bams = bam.collect{"-I $it"}.join(' ')
-  known = knownIndels.collect{"-known $it"}.join(' ')
+  bams = bam.collect{"-I ${it}"}.join(' ')
+  known = knownIndels.collect{"-known ${it}"}.join(' ')
   """
   java -Xmx${task.memory.toGiga()}g \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T IndelRealigner \
-  $bams \
-  -R $genomeFile \
-  -targetIntervals $intervals \
-  $known \
+  ${bams} \
+  -R ${genomeFile} \
+  -targetIntervals ${intervals} \
+  ${known} \
   -nWayOut '.real.bam'
   """
 }
@@ -501,7 +503,7 @@ if (verbose) realignedBam = realignedBam.view {
 process CreateRecalibrationTable {
   tag {idPatient + "-" + idSample}
 
-  publishDir directoryMap.nonRecalibrated, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.nonRecalibrated}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam), file(bai) from realignedBam
@@ -523,19 +525,19 @@ process CreateRecalibrationTable {
   when: step == 'mapping' || step == 'realign'
 
   script:
-  known = knownIndels.collect{ "-knownSites $it" }.join(' ')
+  known = knownIndels.collect{ "-knownSites ${it}" }.join(' ')
   """
   java -Xmx${task.memory.toGiga()}g \
   -Djava.io.tmpdir="/tmp" \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T BaseRecalibrator \
-  -R $genomeFile \
-  -I $bam \
-  -L $intervals \
+  -R ${genomeFile} \
+  -I ${bam} \
+  -L ${intervals} \
   --disable_auto_index_creation_and_locking_when_reading_rods \
-  -knownSites $dbsnp \
-  $known \
-  -nct $task.cpus \
+  -knownSites ${dbsnp} \
+  ${known} \
+  -nct ${task.cpus} \
   -l INFO \
   -o ${idSample}.recal.table
   """
@@ -543,9 +545,9 @@ process CreateRecalibrationTable {
 // Create a TSV file to restart from this step
 recalibrationTableTSV.map { idPatient, status, idSample, bam, bai, recalTable ->
   gender = patientGenders[idPatient]
-  "$idPatient\t$gender\t$status\t$idSample\t$directoryMap.nonRecalibrated/$bam\t$directoryMap.nonRecalibrated/$bai\t\t$directoryMap.nonRecalibrated/$recalTable\n"
+  "${idPatient}\t${gender}\t${status}\t${idSample}\t${params.outDir}/${directoryMap.nonRecalibrated}/${bam}\t${params.outDir}/${directoryMap.nonRecalibrated}/${bai}\t${params.outDir}/${directoryMap.nonRecalibrated}/${recalTable}\n"
 }.collectFile(
-  name: 'nonRecalibrated.tsv', sort: true, storeDir: directoryMap.nonRecalibrated
+  name: 'nonRecalibrated.tsv', sort: true, storeDir: "${params.outDir}/${directoryMap.nonRecalibrated}"
 )
 
 if (step == 'recalibrate') recalibrationTable = bamFiles
@@ -568,10 +570,10 @@ recalTables = recalTables.map { [it[0]] + it[2..-1] } // remove status
 process RecalibrateBam {
   tag {idPatient + "-" + idSample}
 
-  publishDir directoryMap.recalibrated, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.recalibrated}", mode: 'copy'
 
   input:
-    set idPatient, status, idSample, file(bam), file(bai), recalibrationReport from recalibrationTable
+    set idPatient, status, idSample, file(bam), file(bai), file(recalibrationReport) from recalibrationTable
     set file(genomeFile), file(genomeIndex), file(genomeDict), file(intervals) from Channel.value([
       referenceMap.genomeFile,
       referenceMap.genomeIndex,
@@ -592,19 +594,19 @@ process RecalibrateBam {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T PrintReads \
-  -R $genomeFile \
-  -I $bam \
-  -L $intervals \
-  --BQSR $recalibrationReport \
+  -R ${genomeFile} \
+  -I ${bam} \
+  -L ${intervals} \
+  --BQSR ${recalibrationReport} \
   -o ${idSample}.recal.bam
   """
 }
 // Creating a TSV file to restart from this step
 recalibratedBamTSV.map { idPatient, status, idSample, bam, bai ->
   gender = patientGenders[idPatient]
-  "$idPatient\t$gender\t$status\t$idSample\t$directoryMap.recalibrated/$bam\t$directoryMap.recalibrated/$bai\n"
+  "${idPatient}\t${gender}\t${status}\t${idSample}\t${params.outDir}/${directoryMap.recalibrated}/${bam}\t${params.outDir}/${directoryMap.recalibrated}/${bai}\n"
 }.collectFile(
-  name: 'recalibrated.tsv', sort: true, storeDir: directoryMap.recalibrated
+  name: 'recalibrated.tsv', sort: true, storeDir: "${params.outDir}/${directoryMap.recalibrated}"
 )
 
 if (step == 'variantcalling') {
@@ -615,9 +617,7 @@ if (step == 'variantcalling') {
 
   (recalTables, recalibrationTableForHC) = recalTables.into(2)
   recalTables = recalTables.map { [it[0]] + it[2..-1] } // remove status
-} else if (!explicitBqsrNeeded) {
-  (bamForBamQC, bamForSamToolsStats, recalibratedBam) = recalibrationTableForHC.map { it[0..-2] }.into(3)
-}
+} else if (!explicitBqsrNeeded) (bamForBamQC, bamForSamToolsStats, recalibratedBam) = recalibrationTableForHC.map { it[0..-2] }.into(3)
 
 if (verbose) recalibratedBam = recalibratedBam.view {
   "Recalibrated BAM for variant Calling:\n\
@@ -628,7 +628,7 @@ if (verbose) recalibratedBam = recalibratedBam.view {
 process RunSamtoolsStats {
   tag {idPatient + "-" + idSample}
 
-  publishDir directoryMap.samtoolsStats, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.samtoolsStats}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam), file(bai) from bamForSamToolsStats
@@ -636,12 +636,12 @@ process RunSamtoolsStats {
   output:
     file ("${bam}.samtools.stats.out") into samtoolsStatsReport
 
-    when: reports
+  when: reports
 
-    script:
-    """
-    samtools stats $bam > ${bam}.samtools.stats.out
-    """
+  script:
+  """
+  samtools stats ${bam} > ${bam}.samtools.stats.out
+  """
 }
 
 if (verbose) samtoolsStatsReport = samtoolsStatsReport.view {
@@ -652,24 +652,24 @@ if (verbose) samtoolsStatsReport = samtoolsStatsReport.view {
 process RunBamQC {
   tag {idPatient + "-" + idSample}
 
-  publishDir directoryMap.bamQC, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.bamQC}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC
 
   output:
-    file("$idSample") into bamQCreport
+    file("${idSample}") into bamQCreport
 
-    when: reports
+  when: reports && !params.noBAMQC
 
-    script:
-    """
-    qualimap --java-mem-size=${task.memory.toGiga()}G \
-    bamqc \
-    -bam $bam \
-    -outdir $idSample \
-    -outformat HTML
-    """
+  script:
+  """
+  qualimap --java-mem-size=${task.memory.toGiga()}G \
+  bamqc \
+  -bam ${bam} \
+  -outdir ${idSample} \
+  -outformat HTML
+  """
 }
 
 if (verbose) bamQCreport = bamQCreport.view {
@@ -744,14 +744,14 @@ process CreateIntervalBeds {
         longest = t
       chunk += t
       print \$0 > name
-    }' $intervals
+    }' ${intervals}
     """
   else
     """
     awk -vFS="[:-]" '{
       name = sprintf("%s_%d-%d", \$1, \$2, \$3);
       printf("%s\\t%d\\t%d\\n", \$1, \$2-1, \$3) > name ".bed"
-    }' $intervals
+    }' ${intervals}
     """
 }
 
@@ -760,9 +760,8 @@ bedIntervals = bedIntervals
     final duration = 0.0
     for (line in intervalFile.readLines()) {
       final fields = line.split('\t')
-      if (fields.size() >= 5) {
-        duration += fields[4].toFloat()
-      } else {
+      if (fields.size() >= 5) duration += fields[4].toFloat()
+      else {
         start = fields[1].toInteger()
         end = fields[2].toInteger()
         duration += (end - start) / nucleotidesPerSecond
@@ -839,18 +838,18 @@ process RunHaplotypecaller {
   -T HaplotypeCaller \
   --emitRefConfidence GVCF \
   -pairHMM LOGLESS_CACHING \
-  -R $genomeFile \
-  --dbsnp $dbsnp \
-  $BQSR \
-  -I $bam \
-  -L $intervalBed \
+  -R ${genomeFile} \
+  --dbsnp ${dbsnp} \
+  ${BQSR} \
+  -I ${bam} \
+  -L ${intervalBed} \
   --disable_auto_index_creation_and_locking_when_reading_rods \
   -o ${intervalBed.baseName}_${idSample}.g.vcf
   """
 }
 hcGenomicVCF = hcGenomicVCF.groupTuple(by:[0,1,2,3])
 
-if (!gvcf) {hcGenomicVCF.close()}
+if (!gvcf) hcGenomicVCF.close()
 
 process RunGenotypeGVCFs {
   tag {idSample + "-" + intervalBed.baseName}
@@ -876,10 +875,10 @@ process RunGenotypeGVCFs {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T GenotypeGVCFs \
-  -R $genomeFile \
-  -L $intervalBed \
-  --dbsnp $dbsnp \
-  --variant $gvcf \
+  -R ${genomeFile} \
+  -L ${intervalBed} \
+  --dbsnp ${dbsnp} \
+  --variant ${gvcf} \
   --disable_auto_index_creation_and_locking_when_reading_rods \
   -o ${intervalBed.baseName}_${idSample}.vcf
   """
@@ -911,12 +910,12 @@ process RunMutect1 {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$MUTECT_HOME/muTect.jar \
   -T MuTect \
-  -R $genomeFile \
-  --cosmic $cosmic \
-  --dbsnp $dbsnp \
-  -I:normal $bamNormal \
-  -I:tumor $bamTumor \
-  -L $intervalBed \
+  -R ${genomeFile} \
+  --cosmic ${cosmic} \
+  --dbsnp ${dbsnp} \
+  -I:normal ${bamNormal} \
+  -I:tumor ${bamTumor} \
+  -L ${intervalBed} \
   --disable_auto_index_creation_and_locking_when_reading_rods \
   --out ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.call_stats.out \
   --vcf ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
@@ -950,13 +949,13 @@ process RunMutect2 {
   java -Xmx${task.memory.toGiga()}g \
   -jar \$GATK_HOME/GenomeAnalysisTK.jar \
   -T MuTect2 \
-  -R $genomeFile \
-  --cosmic $cosmic \
-  --dbsnp $dbsnp \
-  -I:normal $bamNormal \
-  -I:tumor $bamTumor \
+  -R ${genomeFile} \
+  --cosmic ${cosmic} \
+  --dbsnp ${dbsnp} \
+  -I:normal ${bamNormal} \
+  -I:tumor ${bamTumor} \
   --disable_auto_index_creation_and_locking_when_reading_rods \
-  -L $intervalBed \
+  -L ${intervalBed} \
   -o ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
   """
 }
@@ -978,7 +977,7 @@ process RunFreeBayes {
   script:
   """
   freebayes \
-    -f $genomeFile \
+    -f ${genomeFile} \
     --pooled-continuous \
     --pooled-discrete \
     --genotype-qualities \
@@ -987,9 +986,9 @@ process RunFreeBayes {
     --min-alternate-fraction 0.03 \
     --min-repeat-entropy 1 \
     --min-alternate-count 2 \
-    -t $intervalBed \
-    $bamTumor \
-    $bamNormal > ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
+    -t ${intervalBed} \
+    ${bamTumor} \
+    ${bamNormal} > ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
   """
 }
 
@@ -1008,7 +1007,7 @@ if (verbose) vcfsToMerge = vcfsToMerge.view {
 process ConcatVCF {
   tag {variantCaller in ['gvcf-hc', 'haplotypecaller'] ? variantCaller + "-" + idSampleNormal : variantCaller + "_" + idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir "${directoryMap."$variantCaller"}", mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap."$variantCaller"}", mode: 'copy'
 
   input:
     set variantCaller, idPatient, idSampleNormal, idSampleTumor, file(vcFiles) from vcfsToMerge
@@ -1021,14 +1020,9 @@ process ConcatVCF {
   when: 'haplotypecaller' in tools || 'mutect1' in tools || 'mutect2' in tools || 'freebayes' in tools
 
   script:
-  if (variantCaller == 'haplotypecaller') {
-    outputFile = "${variantCaller}_${idSampleNormal}.vcf"
-  } else if (variantCaller == 'gvcf-hc') {
-    outputFile = "haplotypecaller_${idSampleNormal}.g.vcf"
-  } else {
-    outputFile = "${variantCaller}_${idSampleTumor}_vs_${idSampleNormal}.vcf"
-  }
-  vcfFiles = vcFiles.collect{" $it"}.join(' ')
+  if (variantCaller == 'haplotypecaller') outputFile = "${variantCaller}_${idSampleNormal}.vcf"
+  else if (variantCaller == 'gvcf-hc') outputFile = "haplotypecaller_${idSampleNormal}.g.vcf"
+  else outputFile = "${variantCaller}_${idSampleTumor}_vs_${idSampleNormal}.vcf"
 
   """
   # first make a header from one of the VCF intervals
@@ -1081,7 +1075,7 @@ if (verbose) vcfConcatenated = vcfConcatenated.view {
 process RunStrelka {
   tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir directoryMap.strelka, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.strelka}", mode: 'copy'
 
   input:
     set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor) from bamsForStrelka
@@ -1099,17 +1093,21 @@ process RunStrelka {
   script:
   """
   \$STRELKA_INSTALL_PATH/bin/configureStrelkaSomaticWorkflow.py \
-  --tumor $bamTumor \
-  --normal $bamNormal \
-  --referenceFasta $genomeFile \
+  --tumor ${bamTumor} \
+  --normal ${bamNormal} \
+  --referenceFasta ${genomeFile} \
   --runDir Strelka
 
-  python Strelka/runWorkflow.py -m local -j $task.cpus
+  python Strelka/runWorkflow.py -m local -j ${task.cpus}
 
-  mv Strelka/results/variants/somatic.indels.vcf.gz Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_indels.vcf.gz
-  mv Strelka/results/variants/somatic.indels.vcf.gz.tbi Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_indels.vcf.gz.tbi
-  mv Strelka/results/variants/somatic.snvs.vcf.gz Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_snvs.vcf.gz
-  mv Strelka/results/variants/somatic.snvs.vcf.gz.tbi Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_snvs.vcf.gz.tbi
+  mv Strelka/results/variants/somatic.indels.vcf.gz \
+    Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_indels.vcf.gz
+  mv Strelka/results/variants/somatic.indels.vcf.gz.tbi \
+    Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_indels.vcf.gz.tbi
+  mv Strelka/results/variants/somatic.snvs.vcf.gz \
+    Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_snvs.vcf.gz
+  mv Strelka/results/variants/somatic.snvs.vcf.gz.tbi \
+    Strelka_${idSampleTumor}_vs_${idSampleNormal}_somatic_snvs.vcf.gz.tbi
   """
 }
 
@@ -1123,7 +1121,7 @@ if (verbose) strelkaOutput = strelkaOutput.view {
 process RunSingleStrelka {
   tag {idSample}
 
-  publishDir directoryMap.strelka, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.strelka}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam), file(bai) from bamsForSingleStrelka
@@ -1140,16 +1138,20 @@ process RunSingleStrelka {
   script:
   """
   \$STRELKA_INSTALL_PATH/bin/configureStrelkaGermlineWorkflow.py \
-  --bam $bam \
-  --referenceFasta $genomeFile \
+  --bam ${bam} \
+  --referenceFasta ${genomeFile} \
   --runDir Strelka
 
-  python Strelka/runWorkflow.py -m local -j $task.cpus
+  python Strelka/runWorkflow.py -m local -j ${task.cpus}
 
-  mv Strelka/results/variants/genome.*.vcf.gz Strelka_${idSample}_genome.vcf.gz
-  mv Strelka/results/variants/genome.*.vcf.gz.tbi Strelka_${idSample}_genome.vcf.gz.tbi
-  mv Strelka/results/variants/variants.vcf.gz Strelka_${idSample}_variants.vcf.gz
-  mv Strelka/results/variants/variants.vcf.gz.tbi Strelka_${idSample}_variants.vcf.gz.tbi
+  mv Strelka/results/variants/genome.*.vcf.gz \
+    Strelka_${idSample}_genome.vcf.gz
+  mv Strelka/results/variants/genome.*.vcf.gz.tbi \
+    Strelka_${idSample}_genome.vcf.gz.tbi
+  mv Strelka/results/variants/variants.vcf.gz \
+    Strelka_${idSample}_variants.vcf.gz
+  mv Strelka/results/variants/variants.vcf.gz.tbi \
+    Strelka_${idSample}_variants.vcf.gz.tbi
   """
 }
 
@@ -1163,7 +1165,7 @@ if (verbose) singleStrelkaOutput = singleStrelkaOutput.view {
 process RunManta {
   tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir directoryMap.manta, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.manta}", mode: 'copy'
 
   input:
     set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor) from bamsForManta
@@ -1180,21 +1182,29 @@ process RunManta {
   script:
   """
   \$MANTA_INSTALL_PATH/bin/configManta.py \
-  --normalBam $bamNormal \
-  --tumorBam $bamTumor \
-  --reference $genomeFile \
+  --normalBam ${bamNormal} \
+  --tumorBam ${bamTumor} \
+  --reference ${genomeFile} \
   --runDir Manta
 
-  python Manta/runWorkflow.py -m local -j $task.cpus
-
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSmallIndels.vcf.gz
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSmallIndels.vcf.gz.tbi
-  mv Manta/results/variants/candidateSV.vcf.gz Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSV.vcf.gz
-  mv Manta/results/variants/candidateSV.vcf.gz.tbi Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSV.vcf.gz.tbi
-  mv Manta/results/variants/diploidSV.vcf.gz Manta_${idSampleTumor}_vs_${idSampleNormal}.diploidSV.vcf.gz
-  mv Manta/results/variants/diploidSV.vcf.gz.tbi Manta_${idSampleTumor}_vs_${idSampleNormal}.diploidSV.vcf.gz.tbi
-  mv Manta/results/variants/somaticSV.vcf.gz Manta_${idSampleTumor}_vs_${idSampleNormal}.somaticSV.vcf.gz
-  mv Manta/results/variants/somaticSV.vcf.gz.tbi Manta_${idSampleTumor}_vs_${idSampleNormal}.somaticSV.vcf.gz.tbi
+  python Manta/runWorkflow.py -m local -j ${task.cpus}
+
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSmallIndels.vcf.gz
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSmallIndels.vcf.gz.tbi
+  mv Manta/results/variants/candidateSV.vcf.gz \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSV.vcf.gz
+  mv Manta/results/variants/candidateSV.vcf.gz.tbi \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.candidateSV.vcf.gz.tbi
+  mv Manta/results/variants/diploidSV.vcf.gz \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.diploidSV.vcf.gz
+  mv Manta/results/variants/diploidSV.vcf.gz.tbi \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.diploidSV.vcf.gz.tbi
+  mv Manta/results/variants/somaticSV.vcf.gz \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.somaticSV.vcf.gz
+  mv Manta/results/variants/somaticSV.vcf.gz.tbi \
+    Manta_${idSampleTumor}_vs_${idSampleNormal}.somaticSV.vcf.gz.tbi
   """
 }
 
@@ -1208,7 +1218,7 @@ if (verbose) mantaOutput = mantaOutput.view {
 process RunSingleManta {
   tag {status == 0 ? idSample + " - Single Diploid" : idSample + " - Tumor-Only"}
 
-  publishDir directoryMap.manta, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.manta}", mode: 'copy'
 
   input:
     set idPatient, status, idSample, file(bam), file(bai) from bamsForSingleManta
@@ -1226,34 +1236,46 @@ process RunSingleManta {
   if ( status == 0 ) // If Normal Sample
   """
   \$MANTA_INSTALL_PATH/bin/configManta.py \
-  --bam $bam \
-  --reference $genomeFile \
+  --bam ${bam} \
+  --reference ${genomeFile} \
   --runDir Manta
 
-  python Manta/runWorkflow.py -m local -j $task.cpus
-
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz Manta_${idSample}.candidateSmallIndels.vcf.gz
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${idSample}.candidateSmallIndels.vcf.gz.tbi
-  mv Manta/results/variants/candidateSV.vcf.gz Manta_${idSample}.candidateSV.vcf.gz
-  mv Manta/results/variants/candidateSV.vcf.gz.tbi Manta_${idSample}.candidateSV.vcf.gz.tbi
-  mv Manta/results/variants/diploidSV.vcf.gz Manta_${idSample}.diploidSV.vcf.gz
-  mv Manta/results/variants/diploidSV.vcf.gz.tbi Manta_${idSample}.diploidSV.vcf.gz.tbi
+  python Manta/runWorkflow.py -m local -j ${task.cpus}
+
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz \
+    Manta_${idSample}.candidateSmallIndels.vcf.gz
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
+    Manta_${idSample}.candidateSmallIndels.vcf.gz.tbi
+  mv Manta/results/variants/candidateSV.vcf.gz \
+    Manta_${idSample}.candidateSV.vcf.gz
+  mv Manta/results/variants/candidateSV.vcf.gz.tbi \
+    Manta_${idSample}.candidateSV.vcf.gz.tbi
+  mv Manta/results/variants/diploidSV.vcf.gz \
+    Manta_${idSample}.diploidSV.vcf.gz
+  mv Manta/results/variants/diploidSV.vcf.gz.tbi \
+    Manta_${idSample}.diploidSV.vcf.gz.tbi
   """
   else  // Tumor Sample
   """
   \$MANTA_INSTALL_PATH/bin/configManta.py \
-  --tumorBam $bam \
-  --reference $genomeFile \
+  --tumorBam ${bam} \
+  --reference ${genomeFile} \
   --runDir Manta
 
-  python Manta/runWorkflow.py -m local -j $task.cpus
-
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz Manta_${idSample}.candidateSmallIndels.vcf.gz
-  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi Manta_${idSample}.candidateSmallIndels.vcf.gz.tbi
-  mv Manta/results/variants/candidateSV.vcf.gz Manta_${idSample}.candidateSV.vcf.gz
-  mv Manta/results/variants/candidateSV.vcf.gz.tbi Manta_${idSample}.candidateSV.vcf.gz.tbi
-  mv Manta/results/variants/tumorSV.vcf.gz Manta_${idSample}.tumorSV.vcf.gz
-  mv Manta/results/variants/tumorSV.vcf.gz.tbi Manta_${idSample}.tumorSV.vcf.gz.tbi
+  python Manta/runWorkflow.py -m local -j ${task.cpus}
+
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz \
+    Manta_${idSample}.candidateSmallIndels.vcf.gz
+  mv Manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
+    Manta_${idSample}.candidateSmallIndels.vcf.gz.tbi
+  mv Manta/results/variants/candidateSV.vcf.gz \
+    Manta_${idSample}.candidateSV.vcf.gz
+  mv Manta/results/variants/candidateSV.vcf.gz.tbi \
+    Manta_${idSample}.candidateSV.vcf.gz.tbi
+  mv Manta/results/variants/tumorSV.vcf.gz \
+    Manta_${idSample}.tumorSV.vcf.gz
+  mv Manta/results/variants/tumorSV.vcf.gz.tbi \
+    Manta_${idSample}.tumorSV.vcf.gz.tbi
   """
 }
 
@@ -1285,7 +1307,11 @@ process RunAlleleCount {
 
   script:
   """
-  alleleCounter -l $acLoci -r $genomeFile -b $bam -o ${idSample}.alleleCount;
+  alleleCounter \
+  -l ${acLoci} \
+  -r ${genomeFile} \
+  -b ${bam} \
+  -o ${idSample}.alleleCount;
   """
 }
 
@@ -1308,7 +1334,7 @@ alleleCountOutput = alleleCountOutput.map {
 process RunConvertAlleleCounts {
   tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir directoryMap.ascat, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.ascat}", mode: 'copy'
 
   input:
     set idPatient, idSampleNormal, idSampleTumor, file(alleleCountNormal), file(alleleCountTumor) from alleleCountOutput
@@ -1321,7 +1347,7 @@ process RunConvertAlleleCounts {
   script:
   gender = patientGenders[idPatient]
   """
-  convertAlleleCounts.r $idSampleTumor $alleleCountTumor $idSampleNormal $alleleCountNormal $gender
+  convertAlleleCounts.r ${idSampleTumor} ${alleleCountTumor} ${idSampleNormal} ${alleleCountNormal} ${gender}
   """
 }
 
@@ -1330,7 +1356,7 @@ process RunConvertAlleleCounts {
 process RunAscat {
   tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir directoryMap.ascat, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.ascat}", mode: 'copy'
 
   input:
     set idPatient, idSampleNormal, idSampleTumor, file(bafNormal), file(logrNormal), file(bafTumor), file(logrTumor) from convertAlleleCountsOutput
@@ -1344,7 +1370,7 @@ process RunAscat {
   """
   # get rid of "chr" string if there is any
   for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
-  run_ascat.r $bafTumor $logrTumor $bafNormal $logrNormal $idSampleTumor $baseDir
+  run_ascat.r ${bafTumor} ${logrTumor} ${bafNormal} ${logrNormal} ${idSampleTumor} ${baseDir}
   """
 }
 
@@ -1359,23 +1385,23 @@ vcfNotToAnnotate = Channel.create()
 
 if (step == 'annotate' && annotateVCF == []) {
   Channel.empty().mix(
-    Channel.fromPath('VariantCalling/HaplotypeCaller/*.vcf.gz')
+    Channel.fromPath("${params.outDir}/VariantCalling/HaplotypeCaller/*.vcf.gz")
       .flatten().map{vcf -> ['haplotypecaller',vcf]},
-    Channel.fromPath('VariantCalling/Manta/*SV.vcf.gz')
+    Channel.fromPath("${params.outDir}/VariantCalling/Manta/*SV.vcf.gz")
       .flatten().map{vcf -> ['manta',vcf]},
-    Channel.fromPath('VariantCalling/MuTect1/*.vcf.gz')
+    Channel.fromPath("${params.outDir}/VariantCalling/MuTect1/*.vcf.gz")
       .flatten().map{vcf -> ['mutect1',vcf]},
-    Channel.fromPath('VariantCalling/MuTect2/*.vcf.gz')
+    Channel.fromPath("${params.outDir}/VariantCalling/MuTect2/*.vcf.gz")
       .flatten().map{vcf -> ['mutect2',vcf]},
-    Channel.fromPath('VariantCalling/Strelka/*{somatic,variants}*.vcf.gz')
+    Channel.fromPath("${params.outDir}/VariantCalling/Strelka/*{somatic,variants}*.vcf.gz")
       .flatten().map{vcf -> ['strelka',vcf]}
   ).choice(vcfToAnnotate, vcfNotToAnnotate) { annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1 }
 
 } else if (step == 'annotate' && annotateTools == [] && annotateVCF != []) {
   list = ""
-  annotateVCF.each{ list += ",$it" }
+  annotateVCF.each{ list += ",${it}" }
   list = list.substring(1)
-  if (StringUtils.countMatches("$list", ",") == 0) vcfToAnnotate = Channel.fromPath("$list")
+  if (StringUtils.countMatches("${list}", ",") == 0) vcfToAnnotate = Channel.fromPath("${list}")
     .map{vcf -> ['userspecified',vcf]}
   else vcfToAnnotate = Channel.fromPath("{$list}")
     .map{vcf -> ['userspecified',vcf]}
@@ -1423,7 +1449,7 @@ vcfNotToAnnotate.close()
 process RunBcftoolsStats {
   tag {vcf}
 
-  publishDir directoryMap.bcftoolsStats, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.bcftoolsStats}", mode: 'copy'
 
   input:
     set variantCaller, file(vcf) from vcfForBCFtools
@@ -1435,7 +1461,7 @@ process RunBcftoolsStats {
 
   script:
   """
-  bcftools stats $vcf > ${vcf.baseName}.bcf.tools.stats.out
+  bcftools stats ${vcf} > ${vcf.baseName}.bcf.tools.stats.out
   """
 }
 
@@ -1447,7 +1473,7 @@ if (verbose) bcfReport = bcfReport.view {
 process RunSnpeff {
   tag {vcf}
 
-  publishDir directoryMap.snpeff, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.snpeff}", mode: 'copy'
 
   input:
     set variantCaller, file(vcf) from vcfForSnpeff
@@ -1462,7 +1488,7 @@ process RunSnpeff {
   """
   java -Xmx${task.memory.toGiga()}g \
   -jar \$SNPEFF_HOME/snpEff.jar \
-  $snpeffDb \
+  ${snpeffDb} \
   -csvStats ${vcf.baseName}.snpEff.csv \
   -nodownload \
   -cancer \
@@ -1482,7 +1508,7 @@ if (verbose) snpeffReport = snpeffReport.view {
 process RunVEP {
   tag {vcf}
 
-  publishDir directoryMap.vep, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.vep}", mode: 'copy'
 
   input:
     set variantCaller, file(vcf) from vcfForVep
@@ -1496,7 +1522,7 @@ process RunVEP {
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
   """
   vep \
-  -i $vcf \
+  -i ${vcf} \
   -o ${vcf.baseName}.vep.ann.vcf \
   --stats_file ${vcf.baseName}.vep.summary.html \
   --cache \
@@ -1505,6 +1531,7 @@ process RunVEP {
   --format vcf \
   --offline \
   --pick \
+  --fork ${task.cpus} \
   --total_length \
   --vcf
   """
@@ -1516,7 +1543,7 @@ if (verbose) vepReport = vepReport.view {
 }
 
 process GenerateMultiQCconfig {
-  publishDir directoryMap.multiQC, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.multiQC}", mode: 'copy'
 
   input:
 
@@ -1531,11 +1558,11 @@ process GenerateMultiQCconfig {
   tsvString = step != 'annotate' ? "- TSV file: ${tsvFile}" : ''
   """
   touch multiqc_config.yaml
-  echo "custom_logo: $baseDir/doc/images/CAW_logo.png" >> multiqc_config.yaml
+  echo "custom_logo: ${baseDir}/doc/images/CAW_logo.png" >> multiqc_config.yaml
   echo "custom_logo_url: http://opensource.scilifelab.se/projects/caw" >> multiqc_config.yaml
   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 "- 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: ${workflow.commandLine}" >> multiqc_config.yaml
@@ -1546,17 +1573,17 @@ process GenerateMultiQCconfig {
   echo "- Tools: "${tools.join(", ")} >> multiqc_config.yaml
   echo ${annotateToolString} >> multiqc_config.yaml
   echo ${annotateVCFstring} >> multiqc_config.yaml
-  echo "  acLoci      : $referenceMap.acLoci" >> 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
-  echo "  cosmicIndex : $referenceMap.cosmicIndex" >> multiqc_config.yaml
-  echo "  dbsnp       : $referenceMap.dbsnp" >> multiqc_config.yaml
-  echo "  dbsnpIndex  : $referenceMap.dbsnpIndex" >> multiqc_config.yaml
-  echo "  genomeDict  : $referenceMap.genomeDict" >> multiqc_config.yaml
-  echo "  genomeFile  : $referenceMap.genomeFile" >> multiqc_config.yaml
-  echo "  genomeIndex : $referenceMap.genomeIndex" >> multiqc_config.yaml
-  echo "  intervals   : $referenceMap.intervals" >> multiqc_config.yaml
-  echo "  knownIndels : "${referenceMap.knownIndels.join(", ")} >> multiqc_config.yaml
+  echo "  cosmic      : ${referenceMap.cosmic}" >> multiqc_config.yaml
+  echo "  cosmicIndex : ${referenceMap.cosmicIndex}" >> multiqc_config.yaml
+  echo "  dbsnp       : ${referenceMap.dbsnp}" >> multiqc_config.yaml
+  echo "  dbsnpIndex  : ${referenceMap.dbsnpIndex}" >> multiqc_config.yaml
+  echo "  genomeDict  : ${referenceMap.genomeDict}" >> multiqc_config.yaml
+  echo "  genomeFile  : ${referenceMap.genomeFile}" >> multiqc_config.yaml
+  echo "  genomeIndex : ${referenceMap.genomeIndex}" >> multiqc_config.yaml
+  echo "  intervals   : ${referenceMap.intervals}" >> multiqc_config.yaml
+  echo "  knownIndels : " ${referenceMap.knownIndels.join(", ")} >> multiqc_config.yaml
   echo "  knownIndelsIndex: "${referenceMap.knownIndelsIndex.join(", ")} >> multiqc_config.yaml
   echo "  snpeffDb    : ${params.genomes[params.genome].snpeffDb}" >> multiqc_config.yaml
   echo "top_modules:" >> multiqc_config.yaml
@@ -1576,8 +1603,6 @@ if (verbose && reports) multiQCconfig = multiQCconfig.view {
 
 reportsForMultiQC = Channel.empty()
   .mix(
-    Channel.fromPath('Reports/{BCFToolsStats,MarkDuplicates,SamToolsStats}/*'),
-    Channel.fromPath('Reports/{bamQC,FastQC}/*/*'),
     bamQCreport,
     bcfReport,
     fastQCreport,
@@ -1589,7 +1614,7 @@ reportsForMultiQC = Channel.empty()
   ).collect()
 
 process RunMultiQC {
-  publishDir directoryMap.multiQC, mode: 'copy'
+  publishDir "${params.outDir}/${directoryMap.multiQC}", mode: 'copy'
 
   input:
     file ('*') from reportsForMultiQC
@@ -1597,7 +1622,7 @@ process RunMultiQC {
   output:
     set file("*multiqc_report.html"), file("*multiqc_data") into multiQCReport
 
-    when: reports
+  when: reports
 
   script:
   """
@@ -1619,20 +1644,18 @@ if (verbose) multiQCReport = multiQCReport.view {
 
 def cawMessage() {
   // Display CAW message
-  log.info "CANCER ANALYSIS WORKFLOW ~ $version - " + this.grabRevision() + (workflow.commitId ? " [$workflow.commitId]" : "")
+  log.info "CANCER ANALYSIS WORKFLOW ~ ${version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def checkFileExtension(it, extension) {
   // Check file extension
-  if (!it.toString().toLowerCase().endsWith(extension.toLowerCase())) {
-    exit 1, "File: $it has the wrong extension: $extension see --help for more information"
-  }
+  if (!it.toString().toLowerCase().endsWith(extension.toLowerCase())) exit 1, "File: ${it} has the wrong extension: ${extension} see --help for more information"
 }
 
 def checkParameterExistence(it, list) {
   // Check parameter existence
   if (!list.contains(it)) {
-    println("Unknown parameter: $it")
+    println("Unknown parameter: ${it}")
     return false
   }
   return true
@@ -1644,8 +1667,8 @@ def checkParameterList(list, realList) {
 }
 
 def checkParamReturnFile(item) {
-  params."$item" = params.genomes[params.genome]."$item"
-  return file(params."$item")
+  params."${item}" = params.genomes[params.genome]."${item}"
+  return file(params."${item}")
 }
 
 def checkParams(it) {
@@ -1673,6 +1696,7 @@ def checkParams(it) {
     'dbsnp-index',
     'dbsnp',
     'docker',
+    'genome_base',
     'genome-dict',
     'genome-file',
     'genome-index',
@@ -1687,10 +1711,15 @@ def checkParams(it) {
     'known-indels',
     'knownIndels',
     'knownIndelsIndex',
+    'no-BAMQC',
     'no-GVCF',
     'no-reports',
+    'noBAMQC',
     'noGVCF',
     'noReports',
+    'out-dir',
+    'outDir',
+    'params',
     'project',
     'push',
     'repository',
@@ -1722,15 +1751,12 @@ def checkReferenceMap(referenceMap) {
 }
 
 def checkRefExistence(referenceFile, fileToCheck) {
-  if (fileToCheck instanceof List) {
-    return fileToCheck.every{ checkRefExistence(referenceFile, it) }
-  }
+  if (fileToCheck instanceof List) return fileToCheck.every{ checkRefExistence(referenceFile, it) }
   def f = file(fileToCheck)
-  if (f instanceof List && f.size() > 0) {
-    // this is an expanded wildcard: we can assume all files exist
-    return true
-  } else if (!f.exists()) {
-    log.info  "Missing references: $referenceFile $fileToCheck"
+  // this is an expanded wildcard: we can assume all files exist
+  if (f instanceof List && f.size() > 0) return true
+  else if (!f.exists()) {
+    log.info  "Missing references: ${referenceFile} ${fileToCheck}"
     return false
   }
   return true
@@ -1772,9 +1798,7 @@ def defineDirectoryMap() {
 }
 
 def defineReferenceMap() {
-  if (!(params.genome in params.genomes)) {
-    exit 1, "Genome $params.genome not found in configuration"
-  }
+  if (!(params.genome in params.genomes)) exit 1, "Genome ${params.genome} not found in configuration"
   return [
     // loci file for ascat
     'acLoci'           : checkParamReturnFile("acLoci"),
@@ -1860,8 +1884,8 @@ def extractFastq(tsvFile) {
       // Normally path to files starts from workflow.launchDir
       // But when executing workflow from Github
       // Path to hosted FASTQ files starts from workflow.projectDir
-      def fastqFile1 = workflow.commitId && params.test ? returnFile("$workflow.projectDir/${list[5]}") : returnFile("${list[5]}")
-      def fastqFile2 = workflow.commitId && params.test ? returnFile("$workflow.projectDir/${list[6]}") : returnFile("${list[6]}")
+      def fastqFile1 = workflow.commitId && params.test ? returnFile("${workflow.projectDir}/${list[5]}") : returnFile(list[5])
+      def fastqFile2 = workflow.commitId && params.test ? returnFile("${workflow.projectDir}/${list[6]}") : returnFile(list[6])
 
       checkFileExtension(fastqFile1,".fastq.gz")
       checkFileExtension(fastqFile2,".fastq.gz")
@@ -1881,7 +1905,7 @@ def extractFastqFromDir(pattern) {
   // a temporary channel does all the work
   Channel
     .fromPath(pattern, type: 'dir')
-    .ifEmpty { error "No directories found matching pattern '$pattern'" }
+    .ifEmpty { error "No directories found matching pattern '${pattern}'" }
     .subscribe onNext: { sampleDir ->
       // the last name of the sampleDir is assumed to be a unique sample id
       sampleId = sampleDir.getFileName().toString()
@@ -1889,9 +1913,7 @@ def extractFastqFromDir(pattern) {
       for (path1 in file("${sampleDir}/**_R1_*.fastq.gz")) {
         assert path1.getName().contains('_R1_')
         path2 = file(path1.toString().replace('_R1_', '_R2_'))
-        if (!path2.exists()) {
-            error "Path '${path2}' not found"
-        }
+        if (!path2.exists()) error "Path '${path2}' not found"
         (flowcell, lane) = flowcellLaneFromFastq(path1)
         patient = sampleId
         gender = 'ZZ'  // unused
@@ -2062,44 +2084,48 @@ def isAllowedParams(params) {
 
 def minimalInformationMessage() {
   // Minimal information message
-  log.info "Command Line: $workflow.commandLine"
-  log.info "Project Dir : $workflow.projectDir"
-  log.info "Launch Dir  : $workflow.launchDir"
-  log.info "Work Dir    : $workflow.workDir"
-  if (step != 'annotate') log.info "TSV file    : $tsvFile"
+  log.info "Command Line: " + workflow.commandLine
+  log.info "Profile     : " + workflow.profile
+  log.info "Project Dir : " + workflow.projectDir
+  log.info "Launch Dir  : " + workflow.launchDir
+  log.info "Work Dir    : " + workflow.workDir
+  log.info "Out Dir     : " + params.outDir
+  if (step != 'annotate') log.info "TSV file    : ${tsvFile}"
   log.info "Genome      : " + params.genome
+  log.info "Genome_base : " + params.genome_base
   log.info "Step        : " + step
   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 "Containers  :"
+  if (params.repository) log.info "  Repository   : ${params.repository}"
+  else log.info "  ContainerPath: " + params.containerPath
+  log.info "  Tag          : " + params.tag
   log.info "Reference files used:"
-  log.info "  acLoci      : $referenceMap.acLoci"
-  log.info "  bwaIndex    : " + referenceMap.bwaIndex.join(',\n    ')
-  log.info "  cosmic      : $referenceMap.cosmic"
-  log.info "  cosmicIndex : $referenceMap.cosmicIndex"
-  log.info "  dbsnp       : $referenceMap.dbsnp"
-  log.info "  dbsnpIndex  : $referenceMap.dbsnpIndex"
-  log.info "  genomeDict  : $referenceMap.genomeDict"
-  log.info "  genomeFile  : $referenceMap.genomeFile"
-  log.info "  genomeIndex : $referenceMap.genomeIndex"
-  log.info "  intervals   : $referenceMap.intervals"
-  log.info "  knownIndels : " + referenceMap.knownIndels.join(',\n    ')
-  log.info "  knownIndelsIndex: " + referenceMap.knownIndelsIndex.join(',\n    ')
-  log.info "  snpeffDb    : ${params.genomes[params.genome].snpeffDb}"
+  log.info "  acLoci      :\n\t" + referenceMap.acLoci
+  log.info "  cosmic      :\n\t" + referenceMap.cosmic
+  log.info "\t" + referenceMap.cosmicIndex
+  log.info "  dbsnp       :\n\t" + referenceMap.dbsnp
+  log.info "\t" + referenceMap.dbsnpIndex
+  log.info "  genome      :\n\t" + referenceMap.genomeFile
+  log.info "\t" + referenceMap.genomeDict
+  log.info "\t" + referenceMap.genomeIndex
+  log.info "  bwa indexes :\n\t" + referenceMap.bwaIndex.join(',\n\t')
+  log.info "  intervals   :\n\t" + referenceMap.intervals
+  log.info "  knownIndels :\n\t" + referenceMap.knownIndels.join(',\n\t')
+  log.info "\t" + referenceMap.knownIndelsIndex.join(',\n\t')
+  log.info "  snpeffDb    :\n\t" + params.genomes[params.genome].snpeffDb
 }
 
 def nextflowMessage() {
   // Nextflow message (version + build)
-  log.info "N E X T F L O W  ~  version $workflow.nextflow.version $workflow.nextflow.build"
+  log.info "N E X T F L O W  ~  version ${workflow.nextflow.version} ${workflow.nextflow.build}"
 }
 
 def returnFile(it) {
   // return file if it exists
-  final f = file(it)
-  if (!f.exists()) {
-    exit 1, "Missing file in TSV file: $it, see --help for more information"
-  }
-  return f
+  if (!file(it).exists()) exit 1, "Missing file in TSV file: ${it}, see --help for more information"
+  return file(it)
 }
 
 def returnStatus(it) {
@@ -2107,17 +2133,13 @@ def returnStatus(it) {
   // Status should be only 0 or 1
   // 0 being normal
   // 1 being tumor (or relapse or anything that is not normal...)
-  if (!(it in [0, 1])) {
-    exit 1, "Status is not recognized in TSV file: $it, see --help for more information"
-  }
+  if (!(it in [0, 1])) exit 1, "Status is not recognized in TSV file: ${it}, see --help for more information"
   return it
 }
 
 def returnTSV(it, number) {
   // return TSV if it has the correct number of items in row
-  if (it.size() != number) {
-    exit 1, "Malformed row in TSV file: $it, see --help for more information"
-  }
+  if (it.size() != number) exit 1, "Malformed row in TSV file: ${it}, see --help for more information"
   return it
 }
 
@@ -2130,8 +2152,8 @@ def startMessage() {
 def versionMessage() {
   // Display version message
   log.info "CANCER ANALYSIS WORKFLOW"
-  log.info "  version   : $version"
-  log.info workflow.commitId ? "Git info    : $workflow.repository - $workflow.revision [$workflow.commitId]" : "  revision  : " + this.grabRevision()
+  log.info "  version   : " + version
+  log.info workflow.commitId ? "Git info    : ${workflow.repository} - ${workflow.revision} [${workflow.commitId}]" : "  revision  : " + this.grabRevision()
 }
 
 workflow.onComplete {
@@ -2139,10 +2161,10 @@ workflow.onComplete {
   this.nextflowMessage()
   this.cawMessage()
   this.minimalInformationMessage()
-  log.info "Completed at: $workflow.complete"
-  log.info "Duration    : $workflow.duration"
-  log.info "Success     : $workflow.success"
-  log.info "Exit status : $workflow.exitStatus"
+  log.info "Completed at: " + workflow.complete
+  log.info "Duration    : " + workflow.duration
+  log.info "Success     : " + workflow.success
+  log.info "Exit status : " + workflow.exitStatus
   log.info "Error report: " + (workflow.errorReport ?: '-')
 }
 
@@ -2150,5 +2172,6 @@ workflow.onError {
   // Display error message
   this.nextflowMessage()
   this.cawMessage()
-  log.info "Workflow execution stopped with the following message: " + workflow.errorMessage
+  log.info "Workflow execution stopped with the following message:"
+  log.info "  " + workflow.errorMessage
 }
diff --git a/nextflow.config b/nextflow.config
index a688e115cd..c3d901930c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -23,54 +23,76 @@ env {
   NXF_OPTS="-Xms1g -Xmx4g"
 }
 
+includeConfig 'configuration/base.config'
+
 profiles {
   // Runs the pipeline locally on a single 16-core node
   // Singularity images need to be set up
   standard { // Default profile for UPPMAX secure clusters
     includeConfig 'configuration/uppmax-localhost.config'
     includeConfig 'configuration/singularity-path.config'
+    includeConfig 'configuration/genomes.config'
   }
   // Runs the pipeline using the job scheduler
   // Singularity images need to be set up
   slurm { // slurm profile for UPPMAX secure clusters
     includeConfig 'configuration/uppmax-slurm.config'
     includeConfig 'configuration/singularity-path.config'
+    includeConfig 'configuration/genomes.config'
   }
   // Runs the pipeline locally on a single 16-core node
   // Singularity images will be pulled automatically
   download { // profile for UPPMAX clusters
     includeConfig 'configuration/uppmax-localhost.config'
     includeConfig 'configuration/singularity.config'
+    includeConfig 'configuration/genomes.config'
   }
   // Runs the pipeline using the job scheduler
   // Singularity images will be pulled automatically
   slurm-download { // slurm profile for UPPMAX clusters
     includeConfig 'configuration/uppmax-slurm.config'
     includeConfig 'configuration/singularity.config'
+    includeConfig 'configuration/genomes.config'
   }
   // Docker images will be pulled automatically
   docker { // For small testing testing with Docker
     includeConfig 'configuration/travis.config'
     includeConfig 'configuration/docker.config'
     includeConfig 'configuration/containers.config'
+    includeConfig 'configuration/genomes.config'
   }
+  // Docker images will be pulled automatically
+  awsbatch { // For running on AWS Batch with Docker
+    includeConfig 'configuration/aws-batch.config'
+    includeConfig 'configuration/docker.config'
+    includeConfig 'configuration/containers.config'
+    includeConfig 'configuration/genomes.config'
+   }
   // Singularity images will be pulled automatically
   singularity { // For small testing
     includeConfig 'configuration/travis.config'
     includeConfig 'configuration/singularity.config'
     includeConfig 'configuration/containers.config'
+    includeConfig 'configuration/genomes.config'
+  }
+  // Singularity images need to be set up
+  singularityPath { // For small testing
+    includeConfig 'configuration/travis.config'
+    includeConfig 'configuration/singularity-path.config'
+    includeConfig 'configuration/genomes.config'
   }
 }
 
-// Path to references files
-includeConfig 'configuration/genomes.config'
-
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline { // Turning on timeline tracking by default
   enabled = true
 }
 
+report {  // Turning on execution report by default
+  enabled = true
+}
+
 trace { // Turning on trace tracking by default
   enabled = true
   fields = 'process,task_id,hash,name,attempt,status,exit,realtime,%cpu,vmem,rss,submit,start,complete,duration,realtime,rchar,wchar'
diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index 6da2761064..d8b813f204 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -4,7 +4,7 @@ set -xeuo pipefail
 PROFILE=singularity
 PUSH=''
 REPOSITORY=maxulysse
-TAG=1.2.3
+TAG=1.2.5
 TOOL=docker
 
 while [[ $# -gt 0 ]]
diff --git a/scripts/test.sh b/scripts/test.sh
index ddbba94fd7..fd6358e287 100755
--- a/scripts/test.sh
+++ b/scripts/test.sh
@@ -4,7 +4,7 @@ set -xeuo pipefail
 GENOME=smallGRCh37
 PROFILE=singularity
 SAMPLE=data/tsv/tiny.tsv
-TAG=1.2.3
+TAG=1.2.5
 TEST=ALL
 TRAVIS=${TRAVIS:-false}
 
@@ -45,13 +45,13 @@ 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 --genome_base $PWD/References/$GENOME --verbose
 }
 
 # Build references only for smallGRCh37
 if [[ $GENOME == smallGRCh37 ]] && [[ $TEST != BUILDCONTAINERS ]]
 then
-  nf_test buildReferences.nf --download
+  nf_test buildReferences.nf --download --outDir References/$GENOME
   # Remove images only on TRAVIS
   if [[ $PROFILE == docker ]] && [[ $TRAVIS == true ]]
   then
@@ -85,7 +85,7 @@ fi
 
 if [[ ALL,ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
 then
-  nf_test . --step mapping --sample data/tsv/tiny-single-manta.tsv --tools Manta,Strelka
+  nf_test . --step mapping --sampleDir data/tiny/manta/normal --tools Manta,Strelka
   nf_test . --step mapping --sample data/tsv/tiny-manta.tsv --tools Manta,Strelka
   nf_test . --step mapping --sample $SAMPLE --tools MuTect2
 
@@ -112,7 +112,7 @@ then
   nf_test . --step annotate --tools ${ANNOTATOR} --annotateVCF VariantCalling/Manta/Manta_9876T_vs_1234N.diploidSV.vcf.gz --noReports
 fi
 
-if [[ ALL,BUILDCONTAINERS =~ $TEST ]]
+if [[ ALL,BUILDCONTAINERS =~ $TEST ]] && [[ $PROFILE == docker ]]
 then
   nf_test buildContainers.nf --docker --containers caw,fastqc,gatk,igvtools,multiqc,mutect1,picard,qualimap,runallelecount,r-base,snpeff
 fi