From 141b42fe14563bccaf3997ed07d5f851d0507f89 Mon Sep 17 00:00:00 2001 From: a_anil Date: Fri, 6 Dec 2019 09:39:31 +0100 Subject: [PATCH 01/22] Add nf-core role --- roles/nf-core/defaults/main.yml | 9 +++ roles/nf-core/tasks/main.yml | 72 +++++++++++++++++++ roles/nf-core/templates/site.config.j2 | 27 +++++++ .../templates/irma_ngi_config.yaml.j2 | 2 +- 4 files changed, 109 insertions(+), 1 deletion(-) create mode 100644 roles/nf-core/defaults/main.yml create mode 100644 roles/nf-core/tasks/main.yml create mode 100644 roles/nf-core/templates/site.config.j2 diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml new file mode 100644 index 00000000..d109e002 --- /dev/null +++ b/roles/nf-core/defaults/main.yml @@ -0,0 +1,9 @@ +nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151" +nextflow_version_tag: "v19.04.1" +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 diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml new file mode 100644 index 00000000..138f28ad --- /dev/null +++ b/roles/nf-core/tasks/main.yml @@ -0,0 +1,72 @@ +--- + +- 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: "{{ ansible_env.PATH }}:{{ nf_core_env }}/bin" + 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.0.name }}/singularity-images/{{ item.1 }} {{ ngi_containers }}/{{ item.0.name }}/" + with_subelements: + - "{{ pipelines }}" + - containers + +- 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/main.nf + --custom_config_base {{ sw_path }}{{ item.0.name }}/configs + -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..73f71623 --- /dev/null +++ b/roles/nf-core/templates/site.config.j2 @@ -0,0 +1,27 @@ +process { + {% for i in item.0.containers %} + container = '{{ ngi_containers }}/{{ item.0.name }}/{{ i }}' + {% endfor %} + {% 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 + {% elif item.0.name=='methylseq' %} + genomes { + 'GRCh38' { + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex" + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta" + } + } + {% 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..2af751e3 100644 --- a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 +++ b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 @@ -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/main.nf sthlm_ngi_conf: {{ sthlm_rna_seq_conf }} upps_ngi_conf: {{ upps_rna_seq_conf }} wgs_germline: From 6f1baa9b51b8a9acf587ad1aa166b1708e059dbf Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 21 Jan 2020 11:56:53 +0100 Subject: [PATCH 02/22] Moved rnaseq, methylseq, ampliseq, atacseq to nfcore and upgraded neutronstar, taca amd multiqc --- roles/ampliseq/defaults/main.yml | 7 --- roles/ampliseq/tasks/main.yml | 52 ----------------- roles/ampliseq/templates/ampliseq_site.config | 3 - roles/atacseq/defaults/main.yml | 7 --- roles/atacseq/tasks/main.yml | 52 ----------------- roles/atacseq/templates/atacseq_site.config | 3 - roles/methylseq/defaults/main.yml | 7 --- roles/methylseq/tasks/main.yml | 56 ------------------- .../methylseq/templates/methylseq_site.config | 12 ---- roles/multiqc/defaults/main.yml | 2 +- roles/neutronstar/defaults/main.yml | 2 +- roles/nf-core/defaults/main.yml | 14 ++++- roles/nf-core/tasks/main.yml | 12 ++-- roles/nf-core/templates/site.config.j2 | 11 +--- roles/rnaseq/defaults/main.yml | 7 --- roles/rnaseq/files/install_R_dependencies.r | 12 ---- roles/rnaseq/tasks/main.yml | 52 ----------------- roles/rnaseq/templates/rnaseq_site.config | 6 -- roles/taca/defaults/main.yml | 6 +- 19 files changed, 26 insertions(+), 297 deletions(-) delete mode 100644 roles/ampliseq/defaults/main.yml delete mode 100644 roles/ampliseq/tasks/main.yml delete mode 100644 roles/ampliseq/templates/ampliseq_site.config delete mode 100644 roles/atacseq/defaults/main.yml delete mode 100644 roles/atacseq/tasks/main.yml delete mode 100644 roles/atacseq/templates/atacseq_site.config delete mode 100644 roles/methylseq/defaults/main.yml delete mode 100644 roles/methylseq/tasks/main.yml delete mode 100644 roles/methylseq/templates/methylseq_site.config delete mode 100644 roles/rnaseq/defaults/main.yml delete mode 100644 roles/rnaseq/files/install_R_dependencies.r delete mode 100644 roles/rnaseq/tasks/main.yml delete mode 100644 roles/rnaseq/templates/rnaseq_site.config 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 1ff55e22..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/neutronstar/defaults/main.yml b/roles/neutronstar/defaults/main.yml index c88a4fb6..2cde139c 100644 --- a/roles/neutronstar/defaults/main.yml +++ b/roles/neutronstar/defaults/main.yml @@ -4,7 +4,7 @@ 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" +neutronstar_version: "71f6e3f0377dfb0b4c8324a9cb965d8140869d76" # Temporary variables whilst under dev by Remi neutronstar_container_url: "docker://remiolsen/neutronstar" diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index d109e002..31a25bd8 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -3,7 +3,19 @@ nextflow_version_tag: "v19.04.1" 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 + - 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 diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index 138f28ad..4056192b 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -14,7 +14,7 @@ - name: Install NextFlow local_action: - module: command + module: command _raw_params: "{{ nf_core_env }}/bin/nextflow" environment: NXF_LAUNCHER: "/scratch" @@ -38,7 +38,7 @@ - name: Move singularity images shell: "mv {{ sw_path }}{{ item.0.name }}/singularity-images/{{ item.1 }} {{ ngi_containers }}/{{ item.0.name }}/" - with_subelements: + with_subelements: - "{{ pipelines }}" - containers @@ -54,10 +54,10 @@ lineinfile: dest: "{{ ngi_pipeline_conf }}/{{ item.1.script }}" line: > - alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/main.nf - --custom_config_base {{ sw_path }}{{ item.0.name }}/configs - -profile uppmax - -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.1.site }}.config + alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/main.nf \ + --custom_config_base {{ sw_path }}{{ item.0.name }}/configs \ + -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: diff --git a/roles/nf-core/templates/site.config.j2 b/roles/nf-core/templates/site.config.j2 index 73f71623..84218559 100644 --- a/roles/nf-core/templates/site.config.j2 +++ b/roles/nf-core/templates/site.config.j2 @@ -11,17 +11,10 @@ process { memory = { 62.GB * task.attempt } time = { 2.d * task.attempt } } - {% endif %} + {% endif %} } params { {% if item.0.name=='rnaseq' %} reverse_stranded = true - {% elif item.0.name=='methylseq' %} - genomes { - 'GRCh38' { - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex" - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta" - } - } - {% endif %} + {% endif %} } 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 9936ba4a..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/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 46c22d4f..6adb1821 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -1,7 +1,7 @@ --- 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" @@ -9,8 +9,8 @@ statusdb_version: "ca2a3faea82a10359c70f7a7697db499b5c82b17" 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 From dc62f3bd73ee0e3ad202585b3a0e596190f77e28 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 21 Jan 2020 13:26:01 +0100 Subject: [PATCH 03/22] Updated install.yml with nf-core --- install.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) 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 }}" From 114e370bc139c64f80eb56158d5f99dc1325e960 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 21 Jan 2020 13:55:40 +0100 Subject: [PATCH 04/22] Incorporate past changes --- roles/standalone_scripts/defaults/main.yml | 1 - roles/standalone_scripts/tasks/main.yml | 8 -------- 2 files changed, 9 deletions(-) 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 - From 858b02f5b38e5057ec1c64bf06d859a3ffa379a2 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 23 Jan 2020 11:30:17 +0100 Subject: [PATCH 05/22] Update ngi reports and statusdb versions --- roles/neutronstar/tasks/main.yml | 2 +- roles/ngi_reports/defaults/main.yml | 2 +- roles/taca/defaults/main.yml | 2 +- roles/taca/tasks/main.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index c8fb4110..4ab13b31 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -46,7 +46,7 @@ - { 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 }}" diff --git a/roles/ngi_reports/defaults/main.yml b/roles/ngi_reports/defaults/main.yml index ac4ec2c6..73977cfc 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: 42dddcd8728afc4740643de839aefaa8fcb4fb44 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/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 6adb1821..64e139c9 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -5,7 +5,7 @@ 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" 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 }}" From e243fba2d7c3a3234c535e8ff7aa08cab7feb8fe Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 19:39:45 +0100 Subject: [PATCH 06/22] Update sarek role to move to nf-core --- host_vars/127.0.0.1/main.yml | 4 +--- roles/sarek/defaults/main.yml | 21 +++++++++++---------- roles/sarek/tasks/main.yml | 32 ++++++++++++++++++++++---------- 3 files changed, 34 insertions(+), 23 deletions(-) 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/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..7db9f1aa 100644 --- a/roles/sarek/tasks/main.yml +++ b/roles/sarek/tasks/main.yml @@ -9,25 +9,37 @@ - name: Create sarek containers folder and temp/cache for images file: name="{{ item }}" state=directory mode=g+s with_items: - - "{{ sarek_containers }}/singularity_cache" - - "{{ sarek_containers }}/singularity_temp" + - "sarek/singularity_cache" + - "sarek/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" + SINGULARITY_CACHEDIR: "sarek/singularity_cache" + SINGULARITY_TMPDIR: "sarek/singularity_temp" args: chdir: "{{ sarek_containers }}" - creates: "{{ item }}-{{ sarek_tag }}.img" - with_items: "{{ sarek_containers_images }}" + creates: "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/singularity_cache" + SINGULARITY_TMPDIR: "sarek/singularity_temp" + args: + chdir: "{{ sarek_containers }}" + creates: "{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg" + with_nested: + - "{{ sarek_genome_specific_containers }}" + - "{{ sarek_genomes }}" ignore_errors: true - name: Remove sarek containers temp directories file: name="{{ item }}" state=absent with_items: - - "{{ sarek_containers }}/singularity_cache" - - "{{ sarek_containers }}/singularity_temp" + - "sarek/singularity_cache" + - "sarek/singularity_temp" - name: Deploy irma-specific sarek config copy: From 96eeeead2ffde11c885fd1427fc0b3fd80649a7b Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 20:14:33 +0100 Subject: [PATCH 07/22] Revert "Update sarek role to move to nf-core" This reverts commit e243fba2d7c3a3234c535e8ff7aa08cab7feb8fe. reverting because of conflicts --- host_vars/127.0.0.1/main.yml | 4 +++- roles/sarek/defaults/main.yml | 21 ++++++++++----------- roles/sarek/tasks/main.yml | 32 ++++++++++---------------------- 3 files changed, 23 insertions(+), 34 deletions(-) diff --git a/host_vars/127.0.0.1/main.yml b/host_vars/127.0.0.1/main.yml index e0ef8e84..501436fb 100644 --- a/host_vars/127.0.0.1/main.yml +++ b/host_vars/127.0.0.1/main.yml @@ -44,7 +44,9 @@ 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_tag: "2.5.2" +sarek_repo: "https://github.com/SciLifeLab/sarek.git" +sarek_version: "2.3.FIX1" +sarek_tag: "2.3" sarek_dest: "{{ sw_path }}/sarek" sarek_containers: "{{ ngi_containers }}/sarek" sarek_irma_config: "{{ ngi_pipeline_conf }}/sarek_irma.config" diff --git a/roles/sarek/defaults/main.yml b/roles/sarek/defaults/main.yml index cbdbd9ff..13c21d0c 100644 --- a/roles/sarek/defaults/main.yml +++ b/roles/sarek/defaults/main.yml @@ -1,12 +1,11 @@ --- -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 +sarek_containers_repo: "docker://maxulysse" +sarek_containers_images: + - "sarek" + - "r-base" + - "runallelecount" + - "snpeff" + - "snpeffgrch37" + - "snpeffgrch38" + - "vepgrch37" + - "vepgrch38" diff --git a/roles/sarek/tasks/main.yml b/roles/sarek/tasks/main.yml index 7db9f1aa..de0ef4fd 100644 --- a/roles/sarek/tasks/main.yml +++ b/roles/sarek/tasks/main.yml @@ -9,37 +9,25 @@ - name: Create sarek containers folder and temp/cache for images file: name="{{ item }}" state=directory mode=g+s with_items: - - "sarek/singularity_cache" - - "sarek/singularity_temp" + - "{{ sarek_containers }}/singularity_cache" + - "{{ sarek_containers }}/singularity_temp" -- name: Pull sarek Singularity image - command: "singularity pull --name sarek-{{ sarek_version}}.simg {{ sarek_containers_repo }}/sarek:{{ sarek_version }}" +- name: Pull sarek Singularity images + command: "singularity build {{ item }}-{{ sarek_tag }}.simg {{ sarek_containers_repo }}/{{ item }}:{{ sarek_tag }}" environment: - SINGULARITY_CACHEDIR: "sarek/singularity_cache" - SINGULARITY_TMPDIR: "sarek/singularity_temp" + SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache" + SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp" args: chdir: "{{ sarek_containers }}" - creates: "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/singularity_cache" - SINGULARITY_TMPDIR: "sarek/singularity_temp" - args: - chdir: "{{ sarek_containers }}" - creates: "{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg" - with_nested: - - "{{ sarek_genome_specific_containers }}" - - "{{ sarek_genomes }}" + creates: "{{ item }}-{{ sarek_tag }}.img" + with_items: "{{ sarek_containers_images }}" ignore_errors: true - name: Remove sarek containers temp directories file: name="{{ item }}" state=absent with_items: - - "sarek/singularity_cache" - - "sarek/singularity_temp" + - "{{ sarek_containers }}/singularity_cache" + - "{{ sarek_containers }}/singularity_temp" - name: Deploy irma-specific sarek config copy: From b79ec05e06a7edfec56ef9cfdf42e433cb88072b Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 20:15:24 +0100 Subject: [PATCH 08/22] Revert "Update ngi reports and statusdb versions" This reverts commit 858b02f5b38e5057ec1c64bf06d859a3ffa379a2. reverting because of conflicts --- roles/neutronstar/tasks/main.yml | 2 +- roles/ngi_reports/defaults/main.yml | 2 +- roles/taca/defaults/main.yml | 2 +- roles/taca/tasks/main.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index 4ab13b31..c8fb4110 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -46,7 +46,7 @@ - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" } - { site: "upps", script: "{{ bash_env_upps_script }}" } -- name: Store neutronstar tool version in deployment +- name: Store neutronstar tool version in deployement lineinfile: dest: "{{ deployed_tool_versions }}" line: "neutronstar: {{ neutronstar_version }}" diff --git a/roles/ngi_reports/defaults/main.yml b/roles/ngi_reports/defaults/main.yml index 73977cfc..ac4ec2c6 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: 42dddcd8728afc4740643de839aefaa8fcb4fb44 +ngi_reports_version: 4cd7e236586cc5853f0a58f28edad0a6d5e224a8 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/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 64e139c9..6adb1821 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -5,7 +5,7 @@ taca_ngi_version: 4df67826eea84aef95682570c3bb1ce71890c1fb statusdb_repo: "https://github.com/SciLifeLab/statusdb.git" statusdb_dest: "{{ sw_path }}/statusdb" -statusdb_version: "4100278170269759e65dd0e8801a33787dd5d5c2" +statusdb_version: "ca2a3faea82a10359c70f7a7697db499b5c82b17" flowcell_parser_repo: "https://github.com/SciLifeLab/flowcell_parser.git" flowcell_parser_dest: "{{ sw_path }}/flowcell_parser" diff --git a/roles/taca/tasks/main.yml b/roles/taca/tasks/main.yml index e57bff5e..621cad22 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 deployment +- name: Store taca tools version on deployement lineinfile: dest: "{{ deployed_tool_versions }}" line: "{{ item.tool_name }}: {{ item.tool_version }}" From 187094fed6a134fc61c335cb24a28c23521d4de9 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 20:15:51 +0100 Subject: [PATCH 09/22] Revert "Incorporate past changes" This reverts commit 114e370bc139c64f80eb56158d5f99dc1325e960. reverting because of conflicts --- roles/standalone_scripts/defaults/main.yml | 1 + roles/standalone_scripts/tasks/main.yml | 8 ++++++++ 2 files changed, 9 insertions(+) diff --git a/roles/standalone_scripts/defaults/main.yml b/roles/standalone_scripts/defaults/main.yml index 1671bb20..e03672d7 100644 --- a/roles/standalone_scripts/defaults/main.yml +++ b/roles/standalone_scripts/defaults/main.yml @@ -5,3 +5,4 @@ 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 a11f5639..72585096 100644 --- a/roles/standalone_scripts/tasks/main.yml +++ b/roles/standalone_scripts/tasks/main.yml @@ -13,6 +13,13 @@ 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 $PATH via sourceme @@ -24,3 +31,4 @@ lineinfile: dest={{ ngi_pipeline_conf }}/{{ bash_env_upps_script }} line='export PATH=$PATH:{{ ss_upps_dest }}' backup=no + From 141f7d13069abf739be071ed16229dba6464eeec Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 20:16:03 +0100 Subject: [PATCH 10/22] Revert "Updated install.yml with nf-core" This reverts commit dc62f3bd73ee0e3ad202585b3a0e596190f77e28. reverting because of conflicts --- install.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/install.yml b/install.yml index 83069e6c..e0e6a0f1 100644 --- a/install.yml +++ b/install.yml @@ -38,12 +38,15 @@ - { 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: nf-core, tags: nf-core } + - { role: ampliseq, tags: ampliseq } + - { role: atacseq, tags: atacseq } environment: "{{ anaconda_env }}" From 52094ed9ce62f7a9b8ff723e6ec0ea017b39f5a1 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 24 Jan 2020 20:29:25 +0100 Subject: [PATCH 11/22] Adding changes to sarek, standalone scripts, taca, rnaseq, methylseq, neutronstar, ngi reports --- host_vars/127.0.0.1/main.yml | 4 +- install.yml | 5 +- roles/methylseq/tasks/main.yml | 56 ---------------------- roles/neutronstar/tasks/main.yml | 2 +- roles/ngi_reports/defaults/main.yml | 2 +- roles/rnaseq/tasks/main.yml | 52 -------------------- roles/sarek/defaults/main.yml | 21 ++++---- roles/sarek/tasks/main.yml | 32 +++++++++---- roles/standalone_scripts/defaults/main.yml | 1 - roles/standalone_scripts/tasks/main.yml | 8 ---- roles/taca/defaults/main.yml | 2 +- roles/taca/tasks/main.yml | 2 +- 12 files changed, 39 insertions(+), 148 deletions(-) delete mode 100644 roles/methylseq/tasks/main.yml delete mode 100644 roles/rnaseq/tasks/main.yml 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/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/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index c8fb4110..4ab13b31 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -46,7 +46,7 @@ - { 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 }}" diff --git a/roles/ngi_reports/defaults/main.yml b/roles/ngi_reports/defaults/main.yml index ac4ec2c6..73977cfc 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: 42dddcd8728afc4740643de839aefaa8fcb4fb44 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/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/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..7db9f1aa 100644 --- a/roles/sarek/tasks/main.yml +++ b/roles/sarek/tasks/main.yml @@ -9,25 +9,37 @@ - name: Create sarek containers folder and temp/cache for images file: name="{{ item }}" state=directory mode=g+s with_items: - - "{{ sarek_containers }}/singularity_cache" - - "{{ sarek_containers }}/singularity_temp" + - "sarek/singularity_cache" + - "sarek/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" + SINGULARITY_CACHEDIR: "sarek/singularity_cache" + SINGULARITY_TMPDIR: "sarek/singularity_temp" args: chdir: "{{ sarek_containers }}" - creates: "{{ item }}-{{ sarek_tag }}.img" - with_items: "{{ sarek_containers_images }}" + creates: "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/singularity_cache" + SINGULARITY_TMPDIR: "sarek/singularity_temp" + args: + chdir: "{{ sarek_containers }}" + creates: "{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg" + with_nested: + - "{{ sarek_genome_specific_containers }}" + - "{{ sarek_genomes }}" ignore_errors: true - name: Remove sarek containers temp directories file: name="{{ item }}" state=absent with_items: - - "{{ sarek_containers }}/singularity_cache" - - "{{ sarek_containers }}/singularity_temp" + - "sarek/singularity_cache" + - "sarek/singularity_temp" - name: Deploy irma-specific sarek config copy: 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 6adb1821..64e139c9 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -5,7 +5,7 @@ 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" 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 }}" From 11517b0bf745413317dd024a349b1fe0b86cff9e Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Mon, 27 Jan 2020 13:47:09 +0100 Subject: [PATCH 12/22] Fix issues in new Sarek script and neutronstar --- roles/neutronstar/defaults/main.yml | 4 ++-- roles/sarek/tasks/main.yml | 23 ++++++++++++----------- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/roles/neutronstar/defaults/main.yml b/roles/neutronstar/defaults/main.yml index 2cde139c..ff5b8f73 100644 --- a/roles/neutronstar/defaults/main.yml +++ b/roles/neutronstar/defaults/main.yml @@ -4,8 +4,8 @@ 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: "71f6e3f0377dfb0b4c8324a9cb965d8140869d76" +neutronstar_version: "1.0.0" # Temporary variables whilst under dev by Remi -neutronstar_container_url: "docker://remiolsen/neutronstar" +neutronstar_container_url: "docker://nfcore/neutronstar" neutronstar_image: "neutronstar.simg" diff --git a/roles/sarek/tasks/main.yml b/roles/sarek/tasks/main.yml index 7db9f1aa..cf86e73e 100644 --- a/roles/sarek/tasks/main.yml +++ b/roles/sarek/tasks/main.yml @@ -9,27 +9,28 @@ - name: Create sarek containers folder and temp/cache for images file: name="{{ item }}" state=directory mode=g+s with_items: - - "sarek/singularity_cache" - - "sarek/singularity_temp" + - "{{ sarek_containers }}" + - "{{ sarek_containers }}/singularity_cache" + - "{{ sarek_containers }}/singularity_temp" - name: Pull sarek Singularity image - command: "singularity pull --name sarek-{{ sarek_version}}.simg {{ sarek_containers_repo }}/sarek:{{ sarek_version }}" + command: "singularity pull --name sarek-{{ sarek_version }}.simg {{ sarek_containers_repo }}/sarek:{{ sarek_version }}" environment: - SINGULARITY_CACHEDIR: "sarek/singularity_cache" - SINGULARITY_TMPDIR: "sarek/singularity_temp" + SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache" + SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp" args: chdir: "{{ sarek_containers }}" - creates: "sarek-{{ version }}.simg" + 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/singularity_cache" - SINGULARITY_TMPDIR: "sarek/singularity_temp" + SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache" + SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp" args: chdir: "{{ sarek_containers }}" - creates: "{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg" + creates: "{{ sarek_containers }}/{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg" with_nested: - "{{ sarek_genome_specific_containers }}" - "{{ sarek_genomes }}" @@ -38,8 +39,8 @@ - name: Remove sarek containers temp directories file: name="{{ item }}" state=absent with_items: - - "sarek/singularity_cache" - - "sarek/singularity_temp" + - "{{ sarek_containers }}/singularity_cache" + - "{{ sarek_containers }}/singularity_temp" - name: Deploy irma-specific sarek config copy: From 9d06e12c8533e346c602ec79516e48c2e27a20fe Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 30 Jan 2020 11:14:02 +0100 Subject: [PATCH 13/22] Add supernova and minor changes --- roles/neutronstar/defaults/main.yml | 5 ++++ roles/neutronstar/tasks/main.yml | 26 ++++++++++++++++--- roles/nf-core/defaults/main.yml | 2 +- roles/nf-core/tasks/main.yml | 4 +-- .../templates/irma_ngi_config.yaml.j2 | 20 +++++++------- 5 files changed, 40 insertions(+), 17 deletions(-) diff --git a/roles/neutronstar/defaults/main.yml b/roles/neutronstar/defaults/main.yml index ff5b8f73..2c668b3b 100644 --- a/roles/neutronstar/defaults/main.yml +++ b/roles/neutronstar/defaults/main.yml @@ -9,3 +9,8 @@ neutronstar_version: "1.0.0" # Temporary variables whilst under dev by Remi 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 4ab13b31..a4fca0ea 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: @@ -39,8 +52,8 @@ 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 standard,uppmax \ + -c {{ ngi_pipeline_conf }}/neutronstar_{{ item.site }}.config --supernova_container {{ supernova_container_path }}' backup: no with_items: - { site: "sthlm", script: "{{ bash_env_sthlm_script }}" } @@ -50,3 +63,8 @@ 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/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index 31a25bd8..5c57e2f5 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -1,5 +1,5 @@ nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151" -nextflow_version_tag: "v19.04.1" +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: diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index 4056192b..760555e5 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -24,7 +24,7 @@ - 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: "{{ ansible_env.PATH }}:{{ nf_core_env }}/bin" + PATH: "{{ nf_core_env }}/bin:{{ ansible_env.PATH }}" args: chdir: "{{ sw_path }}" with_items: "{{ pipelines }}" @@ -54,7 +54,7 @@ lineinfile: dest: "{{ ngi_pipeline_conf }}/{{ item.1.script }}" line: > - alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/main.nf \ + alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/ \ --custom_config_base {{ sw_path }}{{ item.0.name }}/configs \ -profile uppmax \ -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.1.site }}.config \ diff --git a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 index 2af751e3..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: {{ sw_path }}rnaseq/workflow/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 }} From 485ac02f06ddee9ad34761b456966b2dfbbbb6c4 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 30 Jan 2020 11:42:18 +0100 Subject: [PATCH 14/22] Syntax bug fix in neutronstar --- roles/neutronstar/tasks/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index a4fca0ea..747b6428 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -11,8 +11,8 @@ with_items: - "{{ neutronstar_container_path }}/singularity_cache" - "{{ neutronstar_container_path }}/singularity_temp" - - "{{ supernova_container_path }}/singularity_cache" - - "{{ supernova_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 }}" From 381e14e86a3b1844a70526b0b66b6d19de00ae14 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Fri, 31 Jan 2020 11:21:08 +0100 Subject: [PATCH 15/22] Update with latest ngi_reports version --- roles/ngi_reports/defaults/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/ngi_reports/defaults/main.yml b/roles/ngi_reports/defaults/main.yml index 73977cfc..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: 42dddcd8728afc4740643de839aefaa8fcb4fb44 +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 }}" From 94b086d5dd978683765f2a8b534c545143359b49 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 4 Feb 2020 11:19:53 +0100 Subject: [PATCH 16/22] Updated neutronstar parameters --- roles/neutronstar/defaults/main.yml | 5 ++--- roles/neutronstar/tasks/main.yml | 2 +- roles/neutronstar/templates/neutronstar_site.config | 6 ++++++ 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/roles/neutronstar/defaults/main.yml b/roles/neutronstar/defaults/main.yml index 2c668b3b..650d8047 100644 --- a/roles/neutronstar/defaults/main.yml +++ b/roles/neutronstar/defaults/main.yml @@ -1,12 +1,11 @@ --- 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: "1.0.0" -# Temporary variables whilst under dev by Remi neutronstar_container_url: "docker://nfcore/neutronstar" neutronstar_image: "neutronstar.simg" diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index 747b6428..4e09b0bc 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -52,7 +52,7 @@ lineinfile: dest: "{{ ngi_pipeline_conf }}/{{ bash_env_sthlm_script }}" line: > - alias neutronstar='nextflow run {{ neutronstar_dest }}/main.nf -profile standard,uppmax \ + 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: diff --git a/roles/neutronstar/templates/neutronstar_site.config b/roles/neutronstar/templates/neutronstar_site.config index 7b0bed96..e2173fef 100644 --- a/roles/neutronstar/templates/neutronstar_site.config +++ b/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' + } From 1728f9c80bfd29c7725c7286b2db68194acfb934 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Wed, 5 Feb 2020 10:42:17 +0100 Subject: [PATCH 17/22] Updated location for downloading multiqc reports on staging env --- roles/multiqc/templates/multiqc_config.yml.j2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/multiqc/templates/multiqc_config.yml.j2 b/roles/multiqc/templates/multiqc_config.yml.j2 index 259ba596..554670e4 100644 --- a/roles/multiqc/templates/multiqc_config.yml.j2 +++ b/roles/multiqc/templates/multiqc_config.yml.j2 @@ -19,7 +19,7 @@ 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 %} From 38ed3cc1d3e1f1a7a3c0354e4d4443739fff4f99 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 6 Feb 2020 14:32:26 +0100 Subject: [PATCH 18/22] Add export_plots to multiqc config --- roles/multiqc/templates/multiqc_config.yml.j2 | 1 + 1 file changed, 1 insertion(+) diff --git a/roles/multiqc/templates/multiqc_config.yml.j2 b/roles/multiqc/templates/multiqc_config.yml.j2 index 554670e4..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 From cac433e97fe4e9b0523f85a253d1615a06adb959 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 13 Feb 2020 14:21:32 +0100 Subject: [PATCH 19/22] Removed container lists in nf-core role --- roles/nf-core/defaults/main.yml | 8 -------- roles/nf-core/tasks/main.yml | 5 ++--- roles/nf-core/templates/site.config.j2 | 6 ++---- 3 files changed, 4 insertions(+), 15 deletions(-) diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index 5c57e2f5..14807636 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -5,17 +5,9 @@ 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 diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index 760555e5..b9b23afc 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -37,10 +37,9 @@ with_items: "{{ pipelines }}" - name: Move singularity images - shell: "mv {{ sw_path }}{{ item.0.name }}/singularity-images/{{ item.1 }} {{ ngi_containers }}/{{ item.0.name }}/" - with_subelements: + shell: "mv {{ sw_path }}{{ item.name }}/singularity-images/nf-core-{{ item.name }}-{{ item.release }}.simg {{ ngi_containers }}/{{ item.name }}/" + with_items: - "{{ pipelines }}" - - containers - name: Create nf-core config template: diff --git a/roles/nf-core/templates/site.config.j2 b/roles/nf-core/templates/site.config.j2 index 84218559..adf3f8a1 100644 --- a/roles/nf-core/templates/site.config.j2 +++ b/roles/nf-core/templates/site.config.j2 @@ -1,7 +1,5 @@ process { - {% for i in item.0.containers %} - container = '{{ ngi_containers }}/{{ item.0.name }}/{{ i }}' - {% endfor %} + 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 } @@ -16,5 +14,5 @@ process { params { {% if item.0.name=='rnaseq' %} reverse_stranded = true - {% endif %} + {% endif %} } From 8c0c66075604699f3ba7ddd5f1deed01117b8fe1 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 13 Feb 2020 15:53:21 +0100 Subject: [PATCH 20/22] Updated neutronstar to use common irma config plus removed custom config base in nf-core --- roles/neutronstar/tasks/main.yml | 1 + .../neutronstar/templates/neutronstar_site.config | 15 +-------------- roles/nf-core/tasks/main.yml | 1 - 3 files changed, 2 insertions(+), 15 deletions(-) diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index 4e09b0bc..b7f66a13 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -53,6 +53,7 @@ dest: "{{ ngi_pipeline_conf }}/{{ bash_env_sthlm_script }}" line: > alias neutronstar='nextflow run {{ neutronstar_dest }}/main.nf -profile singularity \ + -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: diff --git a/roles/neutronstar/templates/neutronstar_site.config b/roles/neutronstar/templates/neutronstar_site.config index e2173fef..ece7a47c 100644 --- a/roles/neutronstar/templates/neutronstar_site.config +++ b/roles/neutronstar/templates/neutronstar_site.config @@ -1,18 +1,5 @@ -process { - container = '{{ neutronstar_container_path }}/{{ neutronstar_image }}' - executor = 'slurm' - 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 - max_cpus = 16 - max_time = 240.h busco_folder = '/sw/apps/bioinfo/BUSCO/v2_lineage_sets' busco_data = 'eukaryota_odb9' diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index b9b23afc..857e5b1f 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -54,7 +54,6 @@ dest: "{{ ngi_pipeline_conf }}/{{ item.1.script }}" line: > alias {{ item.0.name }}='nextflow run {{ sw_path }}{{ item.0.name }}/workflow/ \ - --custom_config_base {{ sw_path }}{{ item.0.name }}/configs \ -profile uppmax \ -c {{ ngi_pipeline_conf }}/nextflow_irma_{{ item.1.site }}.config \ -c {{ ngi_pipeline_conf }}/{{ item.0.name }}_{{ item.1.site }}.config' From 57634203d6c4e283149d53b38d27d3ea76acf77e Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Thu, 13 Feb 2020 16:34:50 +0100 Subject: [PATCH 21/22] Updated neutronstar to use profile uppmax --- roles/neutronstar/tasks/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/neutronstar/tasks/main.yml b/roles/neutronstar/tasks/main.yml index b7f66a13..9e068733 100644 --- a/roles/neutronstar/tasks/main.yml +++ b/roles/neutronstar/tasks/main.yml @@ -52,7 +52,7 @@ lineinfile: dest: "{{ ngi_pipeline_conf }}/{{ bash_env_sthlm_script }}" line: > - alias neutronstar='nextflow run {{ neutronstar_dest }}/main.nf -profile singularity \ + 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 From fc352144df613aea06ed6299cbb5bb48314abe14 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Mon, 17 Feb 2020 14:43:38 +0100 Subject: [PATCH 22/22] Updated nextflow version --- roles/nextflow/defaults/main.yml | 2 +- roles/nf-core/defaults/main.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 index 14807636..099bb162 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -1,5 +1,5 @@ nextflow_java: "/sw/comp/java/x86_64/sun_jdk1.8.0_151" -nextflow_version_tag: "v19.10.0" +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: