diff --git a/host_vars/127.0.0.1/main.yml b/host_vars/127.0.0.1/main.yml
index 501436fb..e0ef8e84 100644
--- a/host_vars/127.0.0.1/main.yml
+++ b/host_vars/127.0.0.1/main.yml
@@ -44,9 +44,7 @@ ngi_pipeline_db_sthlm: "{{ ngi_pipeline_sthlm_path }}/db/records_db_sthlm.sql"
 piper_module_version: 1.5.1
 gatk_bundle_b37: "/sw/data/uppnex/piper_references/2016-04-07/gatk_bundle/2.8/b37/"
 
-sarek_repo: "https://github.com/SciLifeLab/sarek.git"
-sarek_version: "2.3.FIX1"
-sarek_tag: "2.3"
+sarek_tag: "2.5.2"
 sarek_dest: "{{ sw_path }}/sarek"
 sarek_containers: "{{ ngi_containers }}/sarek"
 sarek_irma_config: "{{ ngi_pipeline_conf }}/sarek_irma.config"
diff --git a/install.yml b/install.yml
index e0e6a0f1..83069e6c 100644
--- a/install.yml
+++ b/install.yml
@@ -38,15 +38,12 @@
     - { role: arteria-siswrap-ws, tags: arteria-siswrap }
     - { role: arteria-delivery-ws, tags: arteria-delivery }
     - { role: sarek, tags: sarek }
-    - { role: rnaseq, tags: rnaseq }
-    - { role: methylseq, tags: methylseq }
     - { role: neutronstar, tags: neutronstar }
     - { role: standalone_scripts, tags: standalone_scripts }
     - { role: ugc, tags: ugc }
     - { role: misc-tools, tags: misc-tools }
     - { role: archive-upload-ws, tags: archive-upload }
-    - { role: ampliseq, tags: ampliseq }
-    - { role: atacseq, tags: atacseq }
+    - { role: nf-core, tags: nf-core }
 
   environment: "{{ anaconda_env }}"
 
diff --git a/roles/ampliseq/defaults/main.yml b/roles/ampliseq/defaults/main.yml
deleted file mode 100644
index 9984c439..00000000
--- a/roles/ampliseq/defaults/main.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-ampliseq_repo: "https://github.com/nf-core/ampliseq.git"
-ampliseq_dest: "{{ sw_path }}/ampliseq"
-ampliseq_container_url: "docker://nfcore/ampliseq:{{ ampliseq_version }}"
-ampliseq_container_path: "{{ ngi_containers }}/ampliseq"
-ampliseq_image: "ampliseq-{{ ampliseq_version }}.simg"
-ampliseq_version: "1.1.0"
diff --git a/roles/ampliseq/tasks/main.yml b/roles/ampliseq/tasks/main.yml
deleted file mode 100644
index 028f37e9..00000000
--- a/roles/ampliseq/tasks/main.yml
+++ /dev/null
@@ -1,52 +0,0 @@
----
-
-- name: Fetch nf-core/ampliseq from GitHub
-  git: repo="{{ ampliseq_repo }}"
-       dest="{{ ampliseq_dest }}"
-       version="{{ ampliseq_version }}"
-       force=yes
-
-- name: Create nf-core/ampliseq Singularity folder
-  file: name="{{ ampliseq_container_path }}" state=directory mode=g+s
-
-- name: Create nf-core/ampliseq temp/cache folder for images
-  file: name="{{ item }}" state=directory mode=g+s
-  with_items:
-  - "{{ ampliseq_container_path }}/singularity_cache"
-  - "{{ ampliseq_container_path }}/singularity_temp"
-
-- name: Pull nf-core/ampliseq Singularity image
-  command: "singularity build {{ ampliseq_image }} {{ ampliseq_container_url }}" 
-  environment:
-    SINGULARITY_CACHEDIR: "{{ ampliseq_container_path }}/singularity_cache"
-    SINGULARITY_TMPDIR: "{{ ampliseq_container_path }}/singularity_temp"
-  args:
-    chdir: "{{ ampliseq_container_path }}"
-
-- name: Remove nf-core/ampliseq singularity temp directories
-  file: name="{{ item }}" state=absent
-  with_items:
-  - "{{ ampliseq_container_path }}/singularity_cache"
-  - "{{ ampliseq_container_path }}/singularity_temp"
-
-- name: Create nf-core/ampliseq config
-  template:
-    src: "ampliseq_site.config"
-    dest: "{{ ngi_pipeline_conf }}/ampliseq_{{ item.site }}.config"
-  with_items:
-  - { site: "sthlm", project_id: "{{ ngi_pipeline_sthlm_delivery }}" }
-  - { site: "upps", project_id: "{{ ngi_pipeline_upps_delivery }}" }
-
-
-- name: Set nf-core/ampliseq Bismark alias
-  lineinfile: dest="{{ ngi_pipeline_conf }}/{{ item.script }}"
-              line="alias ampliseq='nextflow run {{ ampliseq_dest }}/ -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.site }}.config -c {{ ngi_pipeline_conf }}/ampliseq_{{ item.site }}.config'"
-              backup=no
-  with_items:
-  - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }
-  - { site: "upps", script: "{{ bash_env_upps_script }}" }
-
-- name: Store ampliseq tool version in deployment
-  lineinfile:
-    dest: "{{ deployed_tool_versions }}"
-    line: "ampliseq: {{ ampliseq_version }}"
diff --git a/roles/ampliseq/templates/ampliseq_site.config b/roles/ampliseq/templates/ampliseq_site.config
deleted file mode 100644
index ee9f65ec..00000000
--- a/roles/ampliseq/templates/ampliseq_site.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
-    container = '{{ ampliseq_container_path }}/{{ ampliseq_image }}'
-}
diff --git a/roles/atacseq/defaults/main.yml b/roles/atacseq/defaults/main.yml
deleted file mode 100644
index af4a2d8c..00000000
--- a/roles/atacseq/defaults/main.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-atacseq_repo: "https://github.com/nf-core/atacseq.git"
-atacseq_dest: "{{ sw_path }}/atacseq"
-atacseq_container_url: "docker://nfcore/atacseq:{{ atacseq_version }}"
-atacseq_container_path: "{{ ngi_containers }}/atacseq"
-atacseq_image: "atacseq-{{ atacseq_version }}.simg"
-atacseq_version: "1.0.0"
diff --git a/roles/atacseq/tasks/main.yml b/roles/atacseq/tasks/main.yml
deleted file mode 100644
index 9139ab2f..00000000
--- a/roles/atacseq/tasks/main.yml
+++ /dev/null
@@ -1,52 +0,0 @@
----
-
-- name: Fetch nf-core/atacseq from GitHub
-  git: repo="{{ atacseq_repo }}"
-       dest="{{ atacseq_dest }}"
-       version="{{ atacseq_version }}"
-       force=yes
-
-- name: Create nf-core/atacseq Singularity folder
-  file: name="{{ atacseq_container_path }}" state=directory mode=g+s
-
-- name: Create nf-core/atacseq temp/cache folder for images
-  file: name="{{ item }}" state=directory mode=g+s
-  with_items:
-  - "{{ atacseq_container_path }}/singularity_cache"
-  - "{{ atacseq_container_path }}/singularity_temp"
-
-- name: Pull nf-core/atacseq Singularity image
-  command: "singularity build {{ atacseq_image }} {{ atacseq_container_url }}" 
-  environment:
-    SINGULARITY_CACHEDIR: "{{ atacseq_container_path }}/singularity_cache"
-    SINGULARITY_TMPDIR: "{{ atacseq_container_path }}/singularity_temp"
-  args:
-    chdir: "{{ atacseq_container_path }}"
-
-- name: Remove nf-core/atacseq singularity temp directories
-  file: name="{{ item }}" state=absent
-  with_items:
-  - "{{ atacseq_container_path }}/singularity_cache"
-  - "{{ atacseq_container_path }}/singularity_temp"
-
-- name: Create nf-core/atacseq config
-  template:
-    src: "atacseq_site.config"
-    dest: "{{ ngi_pipeline_conf }}/atacseq_{{ item.site }}.config"
-  with_items:
-  - { site: "sthlm", project_id: "{{ ngi_pipeline_sthlm_delivery }}" }
-  - { site: "upps", project_id: "{{ ngi_pipeline_upps_delivery }}" }
-
-
-- name: Set nf-core/atacseq Bismark alias
-  lineinfile: dest="{{ ngi_pipeline_conf }}/{{ item.script }}"
-              line="alias atacseq='nextflow run {{ atacseq_dest }}/ -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.site }}.config -c {{ ngi_pipeline_conf }}/atacseq_{{ item.site }}.config'"
-              backup=no
-  with_items:
-  - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }
-  - { site: "upps", script: "{{ bash_env_upps_script }}" }
-
-- name: Store atacseq tool version in deployment
-  lineinfile:
-    dest: "{{ deployed_tool_versions }}"
-    line: "atacseq: {{ atacseq_version }}"
diff --git a/roles/atacseq/templates/atacseq_site.config b/roles/atacseq/templates/atacseq_site.config
deleted file mode 100644
index c9171230..00000000
--- a/roles/atacseq/templates/atacseq_site.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process {
-    container = '{{ atacseq_container_path }}/{{ atacseq_image }}'
-}
diff --git a/roles/methylseq/defaults/main.yml b/roles/methylseq/defaults/main.yml
deleted file mode 100644
index f8178cf5..00000000
--- a/roles/methylseq/defaults/main.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-methylseq_repo: "https://github.com/nf-core/methylseq.git"
-methylseq_dest: "{{ sw_path }}/methylseq"
-methylseq_container_url: "docker://nfcore/methylseq:{{ methylseq_version }}"
-methylseq_container_path: "{{ ngi_containers }}/methylseq"
-methylseq_image: "methylseq-{{ methylseq_version }}.simg"
-methylseq_version: "1.4"
diff --git a/roles/methylseq/tasks/main.yml b/roles/methylseq/tasks/main.yml
deleted file mode 100644
index d4fdb54b..00000000
--- a/roles/methylseq/tasks/main.yml
+++ /dev/null
@@ -1,56 +0,0 @@
----
-
-- name: Fetch nf-core/methylseq from GitHub
-  git: repo="{{ methylseq_repo }}"
-       dest="{{ methylseq_dest }}"
-       version="{{ methylseq_version }}"
-       force=yes
-
-- name: Create nf-core/methylseq Singularity folder
-  file: name="{{ methylseq_container_path }}" state=directory mode=g+s
-
-- name: Create nf-core/methylseq temp/cache folder for images
-  file: name="{{ item }}" state=directory mode=g+s
-  with_items:
-  - "{{ methylseq_container_path }}/singularity_cache"
-  - "{{ methylseq_container_path }}/singularity_temp"
-
-- name: Pull nf-core/methylseq Singularity image
-  command: "singularity build {{ methylseq_image }} {{ methylseq_container_url }}"
-  environment:
-    SINGULARITY_CACHEDIR: "{{ methylseq_container_path }}/singularity_cache"
-    SINGULARITY_TMPDIR: "{{ methylseq_container_path }}/singularity_temp"
-  args:
-    chdir: "{{ methylseq_container_path }}"
-
-- name: Remove nf-core/methylseq singularity temp directories
-  file: name="{{ item }}" state=absent
-  with_items:
-  - "{{ methylseq_container_path }}/singularity_cache"
-  - "{{ methylseq_container_path }}/singularity_temp"
-
-- name: Create nf-core/methylseq config
-  template:
-    src: "methylseq_site.config"
-    dest: "{{ ngi_pipeline_conf }}/methylseq_{{ item.site }}.config"
-  with_items:
-  - { site: "sthlm", project_id: "{{ ngi_pipeline_sthlm_delivery }}" }
-  - { site: "upps", project_id: "{{ ngi_pipeline_upps_delivery }}" }
-
-
-- name: Set nf-core/methylseq Bismark alias
-  lineinfile:
-      dest: "{{ ngi_pipeline_conf }}/{{ item.script }}"
-      line: >
-        alias methylseq='nextflow run {{ methylseq_dest }}/ \
-             -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.site }}.config \
-             -c {{ ngi_pipeline_conf }}/methylseq_{{ item.site }}.config'
-      backup: no
-  with_items:
-  - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }
-  - { site: "upps", script: "{{ bash_env_upps_script }}" }
-
-- name: Store methylseq tool version in deployment
-  lineinfile:
-    dest: "{{ deployed_tool_versions }}"
-    line: "methylseq: {{ methylseq_version }}"
diff --git a/roles/methylseq/templates/methylseq_site.config b/roles/methylseq/templates/methylseq_site.config
deleted file mode 100644
index f3d8c650..00000000
--- a/roles/methylseq/templates/methylseq_site.config
+++ /dev/null
@@ -1,12 +0,0 @@
-process {
-    container = '{{ methylseq_container_path }}/{{ methylseq_image }}'
-
-    // Default memory is less than we have per cpu
-    memory = { 15.GB * task.attempt }
-    time = { 6.h * task.attempt }
-
-    // Large projects seem to need more than default
-    withName:qualimap {
-        time = 4.d
-    }
-}
diff --git a/roles/multiqc/defaults/main.yml b/roles/multiqc/defaults/main.yml
index d07b29f0..9dd0efec 100644
--- a/roles/multiqc/defaults/main.yml
+++ b/roles/multiqc/defaults/main.yml
@@ -1,6 +1,6 @@
 multiqc_repo: https://github.com/ewels/MultiQC.git
 multiqc_dest: "{{ sw_path }}/multiqc"
-multiqc_version: "v1.7"
+multiqc_version: "v1.8"
 
 multiqc_ngi_repo: https://github.com/NationalGenomicsInfrastructure/MultiQC_NGI.git
 multiqc_ngi_dest: "{{ sw_path }}/multiqc_ngi"
diff --git a/roles/multiqc/templates/multiqc_config.yml.j2 b/roles/multiqc/templates/multiqc_config.yml.j2
index 259ba596..499fffbf 100644
--- a/roles/multiqc/templates/multiqc_config.yml.j2
+++ b/roles/multiqc/templates/multiqc_config.yml.j2
@@ -1,5 +1,6 @@
 ---
 no_version_check: True
+export_plots: true
 
 {% if item.site == "upps" %}
 swedac_accredited: False
@@ -19,7 +20,7 @@ remote_destination: 'ngi.web@ngi-internal.scilifelab.se:/var/local/mqc_reports/'
 {% elif deployment_environment == "staging" %}
 remote_sshkey: "/home/funk_007/ssh_keys/id_rsa"
 remote_port: '22'             # Optional
-remote_destination: 'genomics.www@tools-dev.scilifelab.se:/var/local/mqc_reports/'
+remote_destination: 'ngi.web@ngi-internal-dev.scilifelab.se:/home/ngi.web/mqc_reports/'
 megaqc_url: http://megaqc.scilifelab.se/api/upload_parse
 megaqc_access_token: {{ megaqc_token_sthlm_stage }}
 {% endif %}
diff --git a/roles/neutronstar/defaults/main.yml b/roles/neutronstar/defaults/main.yml
index c88a4fb6..650d8047 100644
--- a/roles/neutronstar/defaults/main.yml
+++ b/roles/neutronstar/defaults/main.yml
@@ -1,11 +1,15 @@
 ---
 neutronstar_repo: "https://github.com/nf-core/neutronstar"
 neutronstar_dest: "{{ sw_path }}/neutronstar"
-# neutronstar_container_url: "docker://nf-core/neutronstar:{{ rnaseq_version }}"
+
 neutronstar_container_path: "{{ ngi_containers }}/neutronstar"
-# neutronstar_image: "neutronstar-{{ neutronstar_version }}.simg"
-neutronstar_version: "157a0c904fd5c8de6a174a184aee4a0ac96a871b"
 
-# Temporary variables whilst under dev by Remi
-neutronstar_container_url: "docker://remiolsen/neutronstar"
+neutronstar_version: "1.0.0"
+
+neutronstar_container_url: "docker://nfcore/neutronstar"
 neutronstar_image: "neutronstar.simg"
+
+supernova_container_url: "docker://nfcore/supernova"
+supernova_image: "supernova.simg"
+supernova_version: "2.1.1"
+supernova_container_path: "{{ ngi_containers }}/supernova"
diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml
index c8fb4110..9e068733 100644
--- a/roles/neutronstar/tasks/main.yml
+++ b/roles/neutronstar/tasks/main.yml
@@ -6,11 +6,13 @@
        version="{{ neutronstar_version }}"
        force=yes
 
-- name: Create neutronstar temp/cache folder for images
+- name: Create neutronstar and supernova temp/cache folder for images
   file: name="{{ item }}" state=directory mode=g+s
   with_items:
   - "{{ neutronstar_container_path }}/singularity_cache"
   - "{{ neutronstar_container_path }}/singularity_temp"
+  - "{{ supernova_container_path }}/singularity_cache"
+  - "{{ supernova_container_path }}/singularity_temp"
 
 - name: Pull neutronstar Singularity images
   command: "singularity build {{ neutronstar_image }} {{ neutronstar_container_url }}"
@@ -21,11 +23,22 @@
     chdir: "{{ neutronstar_container_path }}"
   ignore_errors: true
 
-- name: Remove neutronstar singularity temp directories
+- name: Pull supernova Singularity images
+  command: "singularity build {{ supernova_image }} {{ supernova_container_url }}"
+  environment:
+    SINGULARITY_CACHEDIR: "{{ supernova_container_path }}/singularity_cache"
+    SINGULARITY_TMPDIR: "{{ supernova_container_path }}/singularity_temp"
+  args:
+    chdir: "{{ supernova_container_path }}"
+  ignore_errors: true
+
+- name: Remove neutronstar and supernova singularity temp directories
   file: name="{{ item }}" state=absent
   with_items:
   - "{{ neutronstar_container_path }}/singularity_cache"
   - "{{ neutronstar_container_path }}/singularity_temp"
+  - "{{ supernova_container_path }}/singularity_cache"
+  - "{{ supernova_container_path }}/singularity_temp"
 
 - name: Create neutronstar config
   template:
@@ -39,14 +52,20 @@
   lineinfile:
      dest: "{{ ngi_pipeline_conf }}/{{ bash_env_sthlm_script }}"
      line: >
-         alias neutronstar='nextflow run {{ neutronstar_dest }}/main.nf -profile standard,uppmax
-         -c {{ ngi_pipeline_conf }}/neutronstar_{{ item.site }}.config'
+         alias neutronstar='nextflow run {{ neutronstar_dest }}/main.nf -profile uppmax \
+         -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.site }}.config \
+         -c {{ ngi_pipeline_conf }}/neutronstar_{{ item.site }}.config --supernova_container {{ supernova_container_path }}'
      backup: no
   with_items:
   - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }
   - { site: "upps", script: "{{ bash_env_upps_script }}" }
 
-- name: Store neutronstar tool version in deployement
+- name: Store neutronstar tool version in deployment
   lineinfile:
     dest: "{{ deployed_tool_versions }}"
     line: "neutronstar: {{ neutronstar_version }}"
+
+- name: Store supernova tool version in deployment
+  lineinfile:
+    dest: "{{ deployed_tool_versions }}"
+    line: "supernova: {{ supernova_version }}"
diff --git a/roles/neutronstar/templates/neutronstar_site.config b/roles/neutronstar/templates/neutronstar_site.config
index 7b0bed96..ece7a47c 100644
--- a/roles/neutronstar/templates/neutronstar_site.config
+++ b/roles/neutronstar/templates/neutronstar_site.config
@@ -1,13 +1,6 @@
-process {
-    container = '{{ neutronstar_container_path }}/{{ neutronstar_image }}'
-    withName:multiqc {
-        container = null
-        executor = 'local'
-    }
-}
+process.container = '{{ neutronstar_container_path }}/{{ neutronstar_image }}'
 params {
-    project = "{{ item.project_id }}"
-    multiqc_config = "{{ ngi_pipeline_conf }}/multiqc_{{ item.site }}_config.yml"
-    clusterOptions = "-A {{ item.project_id }} -p node"
-    max_memory = 250.GB
+    busco_folder = '/sw/apps/bioinfo/BUSCO/v2_lineage_sets'
+    busco_data = 'eukaryota_odb9'
+
 }
diff --git a/roles/nextflow/defaults/main.yml b/roles/nextflow/defaults/main.yml
index 916f7e36..925282bf 100644
--- a/roles/nextflow/defaults/main.yml
+++ b/roles/nextflow/defaults/main.yml
@@ -1,3 +1,3 @@
 nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151"
-nextflow_version_tag: "v19.04.1"
+nextflow_version_tag: "v20.01.0"
 nextflow_download_url: "https://github.com/nextflow-io/nextflow/releases/download/{{ nextflow_version_tag }}/nextflow"
diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml
new file mode 100644
index 00000000..099bb162
--- /dev/null
+++ b/roles/nf-core/defaults/main.yml
@@ -0,0 +1,13 @@
+nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151"
+nextflow_version_tag: "v20.01.0"
+nextflow_download_url: "https://github.com/nextflow-io/nextflow/releases/download/{{ nextflow_version_tag }}/nextflow"
+nf_core_env: "/lupus/ngi/irma3/nf-core-env"
+pipelines:
+  - name: rnaseq
+    release: 1.4.2
+  - name: methylseq
+    release: 1.4
+  - name: ampliseq
+    release: 1.1.2
+  - name: atacseq
+    release: 1.1.0
diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml
new file mode 100644
index 00000000..857e5b1f
--- /dev/null
+++ b/roles/nf-core/tasks/main.yml
@@ -0,0 +1,70 @@
+---
+
+- name: install nf-core
+  local_action:
+    module: pip
+    virtualenv_command: /lupus/ngi/irma3/virtualenv-15.0.0/virtualenv.py
+    virtualenv: "{{ nf_core_env }}"
+    name: nf-core
+    state: present
+
+- name: Download NextFlow
+  local_action:
+    get_url url="{{ nextflow_download_url }}" dest="{{ nf_core_env }}/bin" mode="u+rwx,g=rwx"
+
+- name: Install NextFlow
+  local_action:
+    module: command
+    _raw_params: "{{ nf_core_env }}/bin/nextflow"
+  environment:
+    NXF_LAUNCHER: "/scratch"
+    NXF_HOME: "{{ nf_core_env }}/nextflow"
+    NXF_WORK: "/scratch"
+
+- name: nf-core
+  command: "{{ nf_core_env }}/bin/nf-core -v download {{ item.name }} --singularity --compress none --outdir {{ sw_path }}{{ item.name }} --release {{ item.release }}"
+  environment:
+    PATH: "{{ nf_core_env }}/bin:{{ ansible_env.PATH }}"
+  args:
+    chdir: "{{ sw_path }}"
+  with_items: "{{ pipelines }}"
+
+- name: Create directories for singularity images
+  file:
+    path: "{{ ngi_containers }}/{{ item.name }}"
+    state: directory
+    mode: g+s
+  with_items: "{{ pipelines }}"
+
+- name: Move singularity images
+  shell: "mv {{ sw_path }}{{ item.name }}/singularity-images/nf-core-{{ item.name }}-{{ item.release }}.simg {{ ngi_containers }}/{{ item.name }}/"
+  with_items:
+    - "{{ pipelines }}"
+
+- name: Create nf-core config
+  template:
+    src: "site.config.j2"
+    dest: "{{ ngi_pipeline_conf }}/{{ item.0.name }}_{{ item.1.site }}.config"
+  with_nested:
+  - "{{ pipelines }}"
+  - [ { site: "sthlm", project_id: "{{ ngi_pipeline_sthlm_delivery }}" }, { site: "upps", project_id: "{{ ngi_pipeline_upps_delivery }}" }]
+
+- name: Set alias for pipeline
+  lineinfile:
+    dest: "{{ ngi_pipeline_conf }}/{{ item.1.script }}"
+    line: >
+          alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/ \
+          -profile uppmax \
+          -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.1.site }}.config \
+          -c {{ ngi_pipeline_conf }}/{{ item.0.name }}_{{ item.1.site }}.config'
+    backup: no
+  with_nested:
+  - "{{ pipelines }}"
+  - [ { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }, { site: "upps", script: "{{ bash_env_upps_script }}" } ]
+
+- name: Store tool version in deployment
+  lineinfile:
+    dest: "{{ deployed_tool_versions }}"
+    line: "{{ item.name }}: {{ item.release }}"
+  with_items:
+  - "{{ pipelines }}"
diff --git a/roles/nf-core/templates/site.config.j2 b/roles/nf-core/templates/site.config.j2
new file mode 100644
index 00000000..adf3f8a1
--- /dev/null
+++ b/roles/nf-core/templates/site.config.j2
@@ -0,0 +1,18 @@
+process {
+  container = '{{ ngi_containers }}/{{ item.0.name }}/nf-core-{{ item.0.name }}-{{ item.0.release }}.simg'
+  {% if item.0.name=='methylseq' %}
+  memory = { 15.GB * task.attempt }
+  time = { 6.h * task.attempt }
+
+  withName:qualimap {
+        cpus = { 4 * task.attempt }
+        memory = { 62.GB * task.attempt }
+        time = { 2.d * task.attempt }
+  }
+  {% endif %}
+}
+params {
+    {% if item.0.name=='rnaseq' %}
+    reverse_stranded = true
+    {% endif %}
+}
diff --git a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
index 0c1a02a3..d522cb70 100644
--- a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
+++ b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
@@ -1,25 +1,25 @@
 # This file should be placed under $HOME/.ngiconfig/ngi_config.yaml
 # or its path exported as the environment variable NGI_CONFIG
 
-# TODO: Deploy the correct version of the database. 
+# TODO: Deploy the correct version of the database.
 database:
     record_tracking_db_path: {{ ngi_pipeline_db }}
 
 environment:
     project_id: {{ ngi_pipeline_slurm_project }}
-    ngi_scripts_dir: {{ ngi_pipeline_dest }}/scripts 
+    ngi_scripts_dir: {{ ngi_pipeline_dest }}/scripts
     conda_env: NGI
     flowcell_inbox:
             - {{ proj_root }}/{{ ngi_pipeline_sthlm_delivery }}/incoming
             - {{ proj_root }}/{{ ngi_pipeline_upps_delivery }}/incoming
-# TODO: This QOS flag is probably not used/needed any longer. 
-#       Enable later in the future if required. 
+# TODO: This QOS flag is probably not used/needed any longer.
+#       Enable later in the future if required.
 
 {% if deployment_environment in [ "staging", "devel" ] %}
 slurm:
      queue: testcore
 {% endif %}
- 
+
 piper:
     #sample:
     #    required_autosomal_coverage: 28.4
@@ -34,7 +34,7 @@ piper:
     #    - arg1
     #    - arg2
     #    - arg3
-    # TODO: Piper module adds setupfilecreator to the path; unsure if this works or if complete path is required.  
+    # TODO: Piper module adds setupfilecreator to the path; unsure if this works or if complete path is required.
     path_to_setupfilecreator: setupfilecreator
     gatk_key: "{{ ngi_resources }}/piper/{{ gatk_key }}"
 
@@ -54,7 +54,7 @@ sarek:
 supported_genomes:
     # GRCh37: Indexed version of "/lupus/data/uppnex/reference/Homo_sapiens/GRCh37/concat/Homo_sapiens.GRCh37.57.dna.concat.fa"
     "GRCh37": "{{ gatk_bundle_b37 }}/human_g1k_v37.fasta"
-    # GRMc38 is currently not used.  
+    # GRMc38 is currently not used.
     #"GRCm38": "/sw/data/uppnex/reference/Mus_musculus/GRCm38/concat/Mus_musculus.GRCm38.69.dna.concat.fa"
     "rn4": None
     "saccer2": None
@@ -74,7 +74,7 @@ analysis:
             analysis_engine: ngi_pipeline.engines.qc_ngi
         RNA-seq:
             analysis_engine: ngi_pipeline.engines.rna_ngi
-            ngi_nf_path: {{ rnaseq_dest }}/main.nf
+            ngi_nf_path: {{ sw_path }}rnaseq/workflow/
             sthlm_ngi_conf: {{ sthlm_rna_seq_conf }}
             upps_ngi_conf: {{ upps_rna_seq_conf }}
         wgs_germline:
@@ -111,8 +111,8 @@ gt_concordance:
     INTERVAL_FILE: {{ ngi_pipeline_dest }}/static/snps.interval_list
     SNPS_FILE: {{ ngi_pipeline_dest }}/static/maf_snps.txt
 
-logging: 
-    log_file: "{{ ngi_pipeline_log }}" 
+logging:
+    log_file: "{{ ngi_pipeline_log }}"
 
 mail:
     recipient: {{ recipient_mail }}
diff --git a/roles/ngi_reports/defaults/main.yml b/roles/ngi_reports/defaults/main.yml
index ac4ec2c6..ab919961 100644
--- a/roles/ngi_reports/defaults/main.yml
+++ b/roles/ngi_reports/defaults/main.yml
@@ -1,7 +1,7 @@
 ---
 ngi_reports_repo: https://github.com/NationalGenomicsInfrastructure/ngi_reports.git
 ngi_reports_dest: "{{ sw_path }}/ngi_reports"
-ngi_reports_version: 4cd7e236586cc5853f0a58f28edad0a6d5e224a8
+ngi_reports_version: 1491800e748b84f1c5a92c64f51af04d72ba0573
 ngi_reports_log: "/log/ngi_reports.log"
 ngi_reports_log_sthlm: "{{ ngi_pipeline_sthlm_path }}/{{ ngi_reports_log }}"
 ngi_reports_log_upps: "{{ ngi_pipeline_upps_path }}/{{ ngi_reports_log }}"
diff --git a/roles/rnaseq/defaults/main.yml b/roles/rnaseq/defaults/main.yml
deleted file mode 100644
index db7c9cab..00000000
--- a/roles/rnaseq/defaults/main.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-rnaseq_repo: "https://github.com/nf-core/rnaseq.git"
-rnaseq_dest: "{{ sw_path }}/rnaseq"
-rnaseq_container_url: "docker://nfcore/rnaseq:{{ rnaseq_version }}"
-rnaseq_container_path: "{{ ngi_containers }}/rnaseq"
-rnaseq_image: "rnaseq-{{ rnaseq_version }}.simg"
-rnaseq_version: "1.4.2"
diff --git a/roles/rnaseq/files/install_R_dependencies.r b/roles/rnaseq/files/install_R_dependencies.r
deleted file mode 100644
index 55f358b3..00000000
--- a/roles/rnaseq/files/install_R_dependencies.r
+++ /dev/null
@@ -1,12 +0,0 @@
-#For edgeR_heatmap_MDS.r
-source("http://bioconductor.org/biocLite.R")
-biocLite("limma", suppressUpdates=TRUE)
-biocLite("edgeR", suppressUpdates=TRUE)
-
-install.packages("data.table", dependencies=TRUE, repos='http://cloud.r-project.org/')
-install.packages("gplots", dependencies=TRUE, repos='http://cloud.r-project.org/')
-
-#For dupRadar.r
-biocLite("dupRadar", suppressUpdates=TRUE)
-
-install.packages("parallel", dependencies=TRUE, repos='http://cloud.r-project.org/')
diff --git a/roles/rnaseq/tasks/main.yml b/roles/rnaseq/tasks/main.yml
deleted file mode 100644
index bc7b3d89..00000000
--- a/roles/rnaseq/tasks/main.yml
+++ /dev/null
@@ -1,52 +0,0 @@
----
-
-- name: Fetch nf-core/rnaseq from GitHub
-  git: repo="{{ rnaseq_repo }}"
-       dest="{{ rnaseq_dest }}"
-       version="{{ rnaseq_version }}"
-       force=yes
-
-- name: Create nf-core/rnaseq temp/cache folder for images
-  file: name="{{ item }}" state=directory mode=g+s
-  with_items:
-  - "{{ rnaseq_container_path }}/singularity_cache"
-  - "{{ rnaseq_container_path }}/singularity_temp"
-
-- name: Pull nf-core/rnaseq Singularity images
-  command: "singularity build {{ rnaseq_image }} {{ rnaseq_container_url }}"
-  environment:
-    SINGULARITY_CACHEDIR: "{{ rnaseq_container_path }}/singularity_cache"
-    SINGULARITY_TMPDIR: "{{ rnaseq_container_path }}/singularity_temp"
-  args:
-    chdir: "{{ rnaseq_container_path }}"
-
-- name: Remove nf-core/rnaseq singularity temp directories
-  file: name="{{ item }}" state=absent
-  with_items:
-  - "{{ rnaseq_container_path }}/singularity_cache"
-  - "{{ rnaseq_container_path }}/singularity_temp"
-
-- name: Create nf-core/rnaseq config
-  template:
-    src: "rnaseq_site.config"
-    dest: "{{ ngi_pipeline_conf }}/rnaseq_{{ item.site }}.config"
-  with_items:
-  - { site: "sthlm", project_id: "{{ ngi_pipeline_sthlm_delivery }}" }
-  - { site: "upps", project_id: "{{ ngi_pipeline_upps_delivery }}" }
-
-- name: Set alias for nf-core/rnaseq
-  lineinfile:
-    dest: "{{ ngi_pipeline_conf }}/{{ item.script }}"
-    line: >
-          alias rnaseq='nextflow run {{ rnaseq_dest }}/ \
-              -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.site }}.config \
-              -c {{ ngi_pipeline_conf }}/rnaseq_{{ item.site }}.config'
-    backup: no
-  with_items:
-  - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" }
-  - { site: "upps", script: "{{ bash_env_upps_script }}" }
-
-- name: Store rnaseq tool version in deployment
-  lineinfile:
-    dest: "{{ deployed_tool_versions }}"
-    line: "rnaseq: {{ rnaseq_version }}"
diff --git a/roles/rnaseq/templates/rnaseq_site.config b/roles/rnaseq/templates/rnaseq_site.config
deleted file mode 100644
index d0f00315..00000000
--- a/roles/rnaseq/templates/rnaseq_site.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-    container = '{{ rnaseq_container_path }}/{{ rnaseq_image }}'
-}
-params {
-    reverse_stranded = true
-}
diff --git a/roles/sarek/defaults/main.yml b/roles/sarek/defaults/main.yml
index 13c21d0c..cbdbd9ff 100644
--- a/roles/sarek/defaults/main.yml
+++ b/roles/sarek/defaults/main.yml
@@ -1,11 +1,12 @@
 ---
-sarek_containers_repo: "docker://maxulysse"
-sarek_containers_images:
-    - "sarek"
-    - "r-base"
-    - "runallelecount"
-    - "snpeff"
-    - "snpeffgrch37"
-    - "snpeffgrch38"
-    - "vepgrch37"
-    - "vepgrch38"
+sarek_containers_repo: "docker://nfcore"
+sarek_repo: "https://github.com/nf-core/sarek.git"
+sarek_version: "2.5.2"
+sarek_genome_specific_containers:
+  - sarekvep
+  - sareksnpeff
+sarek_genomes:
+  - GRCh38
+  - GRCh37
+  - GRCm38
+  - CanFam3.1
diff --git a/roles/sarek/tasks/main.yml b/roles/sarek/tasks/main.yml
index de0ef4fd..cf86e73e 100644
--- a/roles/sarek/tasks/main.yml
+++ b/roles/sarek/tasks/main.yml
@@ -9,18 +9,31 @@
 - name: Create sarek containers folder and temp/cache for images
   file: name="{{ item }}" state=directory mode=g+s
   with_items:
+  - "{{ sarek_containers }}"
   - "{{ sarek_containers }}/singularity_cache"
   - "{{ sarek_containers }}/singularity_temp"
 
-- name: Pull sarek Singularity images
-  command: "singularity build {{ item }}-{{ sarek_tag }}.simg {{ sarek_containers_repo }}/{{ item }}:{{ sarek_tag }}"
+- name: Pull sarek Singularity image
+  command: "singularity pull --name sarek-{{ sarek_version }}.simg {{ sarek_containers_repo }}/sarek:{{ sarek_version }}"
   environment:
     SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache"
     SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp"
   args:
     chdir: "{{ sarek_containers }}"
-    creates: "{{ item }}-{{ sarek_tag }}.img"
-  with_items: "{{ sarek_containers_images }}"
+    creates: "{{ sarek_containers }}/saresarek-{{ sarek_version }}.simg"
+  ignore_errors: true
+
+- name: Pull sarekvep, sareksnpeff Singularity images
+  command: "singularity pull --name {{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg {{ sarek_containers_repo }}/{{ item.0 }}:{{ sarek_version }}.{{ item.1 }}"
+  environment:
+    SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache"
+    SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp"
+  args:
+    chdir: "{{ sarek_containers }}"
+    creates: "{{ sarek_containers }}/{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg"
+  with_nested:
+    - "{{ sarek_genome_specific_containers }}"
+    - "{{ sarek_genomes }}"
   ignore_errors: true
 
 - name: Remove sarek containers temp directories
diff --git a/roles/standalone_scripts/defaults/main.yml b/roles/standalone_scripts/defaults/main.yml
index e03672d7..1671bb20 100644
--- a/roles/standalone_scripts/defaults/main.yml
+++ b/roles/standalone_scripts/defaults/main.yml
@@ -5,4 +5,3 @@ ss_sthlm_dest: "{{ sw_path }}/standalone_scripts"
 ss_upps_repo: "https://github.com/Molmed/irma-scripts.git"
 ss_upps_dest: "{{ sw_path }}/upps_standalone_scripts"
 ss_upps_version: "master"
-ss_upps_local_dest: "{{ proj_root }}/{{ ngi_pipeline_upps_delivery }}/private/scripts"
\ No newline at end of file
diff --git a/roles/standalone_scripts/tasks/main.yml b/roles/standalone_scripts/tasks/main.yml
index 72585096..a11f5639 100644
--- a/roles/standalone_scripts/tasks/main.yml
+++ b/roles/standalone_scripts/tasks/main.yml
@@ -13,13 +13,6 @@
        version="{{ ss_upps_version }}"
        force=yes
 
-# Symlink the upps scripts to the local project
-- name: Symlink upps standalone scripts
-  file:
-    src: "{{ ss_upps_dest }}"
-    dest: "{{ ss_upps_local_dest }}"
-    state: link
-
 # Since the standalone repo is more free-form than others
 # putting PATH at end of $PATH as a safeguard from future problems
 - name: Add standalone scripts to end of sthlm's $PATH via sourceme
@@ -31,4 +24,3 @@
   lineinfile: dest={{ ngi_pipeline_conf }}/{{ bash_env_upps_script }}
               line='export PATH=$PATH:{{ ss_upps_dest }}'
               backup=no
-
diff --git a/roles/taca/defaults/main.yml b/roles/taca/defaults/main.yml
index 46c22d4f..64e139c9 100644
--- a/roles/taca/defaults/main.yml
+++ b/roles/taca/defaults/main.yml
@@ -1,16 +1,16 @@
 ---
 taca_ngi_repo: https://github.com/SciLifeLab/taca-ngi-pipeline.git
 taca_ngi_dest: "{{ sw_path }}/taca-ngi-pipeline"
-taca_ngi_version: b9ed0c748bcbb0bfe6b1106e5dc2778f73b936a2
+taca_ngi_version: 4df67826eea84aef95682570c3bb1ce71890c1fb
 
 statusdb_repo: "https://github.com/SciLifeLab/statusdb.git"
 statusdb_dest: "{{ sw_path }}/statusdb"
-statusdb_version: "ca2a3faea82a10359c70f7a7697db499b5c82b17"
+statusdb_version: "4100278170269759e65dd0e8801a33787dd5d5c2"
 
 flowcell_parser_repo: "https://github.com/SciLifeLab/flowcell_parser.git"
 flowcell_parser_dest: "{{ sw_path }}/flowcell_parser"
-flowcell_parser_version: "e4750ce700026b1e7427de712d1464049d222a88"
+flowcell_parser_version: "39224d94cf3d6b6547ae06012f54b664a22e8fac"
 
 taca_repo: "https://github.com/SciLifeLab/TACA.git"
 taca_dest: "{{ sw_path }}/TACA"
-taca_version: dd76b0699766d8cc42db4f0b20ebb1a979c6cc6b
+taca_version: b0e4e0a658fa0eda39f8f7999ea0a32148c9a865
diff --git a/roles/taca/tasks/main.yml b/roles/taca/tasks/main.yml
index 621cad22..e57bff5e 100644
--- a/roles/taca/tasks/main.yml
+++ b/roles/taca/tasks/main.yml
@@ -59,7 +59,7 @@
 - name: Deploy runfolder delivery stockholm config
   template: src="site_taca_runfolder_delivery.yml.j2" dest="{{ ngi_pipeline_conf }}/TACA/{{ site }}_taca_runfolder_delivery.yml"
 
-- name: Store taca tools version on deployement
+- name: Store taca tools version on deployment
   lineinfile:
     dest: "{{ deployed_tool_versions }}"
     line: "{{ item.tool_name }}: {{ item.tool_version }}"