New nf-core role to pull methylseq, rnaseq, atacseq etc and other changes

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"

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 }}"
 

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"

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"

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 +52,19 @@
   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 singularity \
+         -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 }}"

roles/neutronstar/templates/neutronstar_site.config

@@ -1,5 +1,6 @@
 process {
     container = '{{ neutronstar_container_path }}/{{ neutronstar_image }}'
+    executor = 'slurm'
     withName:multiqc {
         container = null
         executor = 'local'
@@ -10,4 +11,9 @@ params {
     multiqc_config = "{{ ngi_pipeline_conf }}/multiqc_{{ item.site }}_config.yml"
     clusterOptions = "-A {{ item.project_id }} -p node"
     max_memory = 250.GB
+    max_cpus = 16
+    max_time = 240.h
+    busco_folder = '/sw/apps/bioinfo/BUSCO/v2_lineage_sets'
+    busco_data = 'eukaryota_odb9'
+
 }

roles/nf-core/defaults/main.yml

@@ -0,0 +1,21 @@
+nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151"
+nextflow_version_tag: "v19.10.0"
+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
+    containers:
+      - nf-core-rnaseq-1.4.2.simg
+  - name: methylseq
+    release: 1.4
+    containers:
+      - nf-core-methylseq-1.4.simg
+  - name: ampliseq
+    release: 1.1.2
+    containers:
+      - nf-core-ampliseq-1.1.2.simg
+  - name: atacseq
+    release: 1.1.0
+    containers:
+      - nf-core-atacseq-1.1.0.simg