From 98af62bebe9a6746c5cdb4e892812919b81d7237 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Jan 2025 13:35:26 +0100 Subject: [PATCH 1/5] Use ngi fork for nf-core/rnaseq --- host_vars/deploy/main.yml | 2 +- roles/nf-core/defaults/main.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/host_vars/deploy/main.yml b/host_vars/deploy/main.yml index ac4b3803..85dffa9d 100644 --- a/host_vars/deploy/main.yml +++ b/host_vars/deploy/main.yml @@ -47,7 +47,7 @@ ngi_resources: "{{ root_path }}/resources/" sarek_tag: "3.4.2" sarek_dest: "{{ sw_path }}/sarek/{{ sarek_tag | replace('.', '_') }}" -rnaseq_tag: "3.12.0" +rnaseq_tag: "3.12.0_ngi_v1-rc1" rnaseq_dest: "{{ sw_path }}/rnaseq/{{ rnaseq_tag | replace('.', '_') }}" demultiplex_tag: "1.5.4" diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index 033ab6f5..b2bf915d 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -16,7 +16,7 @@ nf_core_vars: PATH: "{{ nf_core_env }}/bin:{{ tools_path.PATH }}" biocontainers_dirname: biocontainers pipelines: - - name: rnaseq + - name: NationalGenomicsInfrastructure/nfcore_rnaseq release: "{{ rnaseq_tag }}" container_dir: "{{ biocontainers_dirname }}" - name: sarek @@ -89,4 +89,4 @@ igenomes: build: GRCh38 type: gatk -ncbi_eutils_url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils \ No newline at end of file +ncbi_eutils_url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils From 631441f7cb0be443c2ac73949916777ca801adda Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Jan 2025 13:57:16 +0100 Subject: [PATCH 2/5] Fix rnaseq version number --- host_vars/deploy/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/host_vars/deploy/main.yml b/host_vars/deploy/main.yml index 85dffa9d..4c2a780c 100644 --- a/host_vars/deploy/main.yml +++ b/host_vars/deploy/main.yml @@ -47,7 +47,7 @@ ngi_resources: "{{ root_path }}/resources/" sarek_tag: "3.4.2" sarek_dest: "{{ sw_path }}/sarek/{{ sarek_tag | replace('.', '_') }}" -rnaseq_tag: "3.12.0_ngi_v1-rc1" +rnaseq_tag: "v3.12.0_ngi_v1-rc1" rnaseq_dest: "{{ sw_path }}/rnaseq/{{ rnaseq_tag | replace('.', '_') }}" demultiplex_tag: "1.5.4" From 5956e5a82f8aca97a600bb35e36d2d8b07ca2619 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Wed, 8 Jan 2025 14:18:48 +0100 Subject: [PATCH 3/5] Define repository variable for rnaseq --- roles/nf-core/defaults/main.yml | 3 ++- roles/nf-core/tasks/main.yml | 1 + roles/nf-core/tasks/pipeline.yml | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index b2bf915d..8d05fd82 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -16,9 +16,10 @@ nf_core_vars: PATH: "{{ nf_core_env }}/bin:{{ tools_path.PATH }}" biocontainers_dirname: biocontainers pipelines: - - name: NationalGenomicsInfrastructure/nfcore_rnaseq + - name: rnaseq release: "{{ rnaseq_tag }}" container_dir: "{{ biocontainers_dirname }}" + repository: NationalGenomicsInfrastructure/nfcore_rnaseq - name: sarek release: "{{ sarek_tag }}" container_dir: "{{ biocontainers_dirname }}" diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index eae36ff1..306fddc8 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -17,6 +17,7 @@ pipeline_genomes: "{{ item.pipeline_genomes | default([]) }}" extra_parameters: "{{ item.extra_parameters | default({}) }}" container_dir: "{{ ngi_containers }}/{{ item.container_dir | default(item.name) }}" + repository: "{{ item.repository | default(item.name) }}" with_items: "{{ pipelines }}" tags: pipelines diff --git a/roles/nf-core/tasks/pipeline.yml b/roles/nf-core/tasks/pipeline.yml index a12e1551..b5a90377 100644 --- a/roles/nf-core/tasks/pipeline.yml +++ b/roles/nf-core/tasks/pipeline.yml @@ -17,7 +17,7 @@ - name: nf-core download {{ pipeline }} v{{ release }} command: > nf-core -v - download {{ pipeline }} + pipeline download {{ repository }} -d --compress none --outdir {{ sw_path }}/{{ pipeline }} @@ -94,4 +94,4 @@ - name: store {{ pipeline }} version in deployment lineinfile: dest: "{{ deployed_tool_versions }}" - line: "{{ pipeline }}: {{ release }}" \ No newline at end of file + line: "{{ pipeline }}: {{ release }}" From de3bd840259f2f52874d95149df09d23fee7356f Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 9 Jan 2025 10:14:37 +0100 Subject: [PATCH 4/5] Update nf-core/tools to 3.0.2 - 3.1.1 is not available on bioconda yet - Requires nextflow >=24.0.4 --- roles/nextflow/defaults/main.yml | 2 +- roles/nf-core/defaults/main.yml | 2 +- roles/nf-core/tasks/pipeline.yml | 13 +++++++------ 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/roles/nextflow/defaults/main.yml b/roles/nextflow/defaults/main.yml index bdd1ab19..86b0adc3 100644 --- a/roles/nextflow/defaults/main.yml +++ b/roles/nextflow/defaults/main.yml @@ -1,6 +1,6 @@ java_home: /sw/comp/java/x86_64/OracleJDK_11.0.9 nextflow_java: "{{ java_home }}" -nextflow_version_tag: 24.04.1 +nextflow_version_tag: 24.04.4 nextflow_download_url: https://github.com/nextflow-io/nextflow/releases/download/v{{ nextflow_version_tag }}/nextflow nf_schema_version: 2.1.1 nextflow_local_env: diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index 8d05fd82..ebd0abc2 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -1,6 +1,6 @@ nf_core_env_name: nf-core-env nf_core_env: "{{ sw_path }}/anaconda/envs/{{ nf_core_env_name }}" -nf_core_version: 2.14.1 +nf_core_version: 3.0.2 nf_core_container_repo: docker://nfcore nf_core_vars: NFCORE_NO_VERSION_CHECK: 1 diff --git a/roles/nf-core/tasks/pipeline.yml b/roles/nf-core/tasks/pipeline.yml index b5a90377..2ec03b80 100644 --- a/roles/nf-core/tasks/pipeline.yml +++ b/roles/nf-core/tasks/pipeline.yml @@ -14,23 +14,24 @@ loop_control: loop_var: cachedir -- name: nf-core download {{ pipeline }} v{{ release }} +- name: nf-core download {{ pipeline }} {{ release }} command: > nf-core -v - pipeline download {{ repository }} - -d + pipelines download {{ repository }} + --download-configuration yes --compress none --outdir {{ sw_path }}/{{ pipeline }} --revision {{ release }} --container-system singularity --container-cache-utilisation amend + --parallel-downloads 4 environment: "{{ nf_core_vars }}" ignore_errors: true args: chdir: "{{ sw_path }}" creates: "{{ sw_path }}/{{ pipeline }}/{{ release | replace('.', '_') }}" -- name: pull pipeline-specific images for {{ pipeline }} v{{ release }} +- name: pull pipeline-specific images for {{ pipeline }} {{ release }} command: "singularity pull --name nfcore-{{ container.0 }}.{{ container.1 }}.img {{ nf_core_container_repo }}/{{ container.0 | replace('-', ':', 1) }}.{{ container.1 }}" environment: "{{ nf_core_vars }}" args: @@ -43,12 +44,12 @@ loop_control: loop_var: container -- name: create nf-core {{ pipeline }} v{{ release }} config +- name: create nf-core {{ pipeline }} {{ release }} config template: src: "site.config.j2" dest: "{{ ngi_pipeline_conf }}/{{ pipeline }}_{{ site }}.config" -- name: set alias for pipeline {{ pipeline }} v{{ release }} +- name: set alias for pipeline {{ pipeline }} {{ release }} lineinfile: dest: "{{ ngi_pipeline_conf }}/{{ bash_env_script }}" line: > From a8d0992799625fe6f2d02c04ca1b42a286a84037 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 9 Jan 2025 13:32:24 +0100 Subject: [PATCH 5/5] Update nf-core/ampliseq to 2.12.0 --- roles/nf-core/defaults/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index ebd0abc2..a4a1ce75 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -45,7 +45,7 @@ pipelines: accession: NC_001416.1 sha1: 2b03cbf38a8e6816914b172f048a2fe896317df7 - name: ampliseq - release: 2.5.0 + release: 2.12.0 extra_parameters: silva_base_url: https://www.arb-silva.de/fileadmin/silva_databases/qiime silva_zip: Silva_132_release.zip