Merge pull request #332 from aanil/master

New nf-core role to pull methylseq, rnaseq, atacseq etc and other changes
NationalGenomicsInfrastructure · Feb 17, 2020 · b0dd84f · b0dd84f
2 parents bcaf5cd + fc35214
commit b0dd84f
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Showing 32 changed files with 188 additions and 346 deletions.
diff --git 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
@@ -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
diff --git a/roles/ampliseq/tasks/main.yml b/roles/ampliseq/tasks/main.yml
diff --git a/roles/ampliseq/templates/ampliseq_site.config b/roles/ampliseq/templates/ampliseq_site.config
diff --git a/roles/atacseq/defaults/main.yml b/roles/atacseq/defaults/main.yml
diff --git a/roles/atacseq/tasks/main.yml b/roles/atacseq/tasks/main.yml
diff --git a/roles/atacseq/templates/atacseq_site.config b/roles/atacseq/templates/atacseq_site.config
diff --git a/roles/methylseq/defaults/main.yml b/roles/methylseq/defaults/main.yml
diff --git a/roles/methylseq/tasks/main.yml b/roles/methylseq/tasks/main.yml
diff --git a/roles/methylseq/templates/methylseq_site.config b/roles/methylseq/templates/methylseq_site.config
diff --git 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
@@ -1,5 +1,6 @@
 ---
 no_version_check: True
+export_plots: true
 
 {% if item.site == "upps" %}
 swedac_accredited: False
@@ -19,7 +20,7 @@ remote_destination: '[email protected]:/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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