From d1e5658a042dc1157ef3f9299d2f2d37075755c4 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 26 May 2020 16:55:40 +0200 Subject: [PATCH 1/3] Fix location for ampliseq classifier --- roles/nf-core/tasks/main.yml | 4 ++-- roles/nf-core/templates/site.config.j2 | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index c4da6669..af7d1be6 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -23,7 +23,7 @@ - name: Create temp directories for singularity images file: - path: "{{ item }}" + path: "{{ item }}" state: directory with_items: - "{{ ngi_containers }}/singularity_cache" @@ -81,7 +81,7 @@ - name: Download SILVA classifier data for ampliseq get_url: url: https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip - dest: "{{ ngi_resources }}ampliseq/Silva_132_release.zip" + dest: "{{ ngi_rcontainers }}/ampliseq/Silva_132_release.zip" - name: Store tool version in deployment lineinfile: diff --git a/roles/nf-core/templates/site.config.j2 b/roles/nf-core/templates/site.config.j2 index 991eb685..a371cb82 100644 --- a/roles/nf-core/templates/site.config.j2 +++ b/roles/nf-core/templates/site.config.j2 @@ -22,5 +22,5 @@ process { params.reverseStranded = true {% endif %} {% if item.0.name=='ampliseq' %} -params.reference_database = '{{ ngi_resources }}ampliseq/Silva_132_release.zip' +params.reference_database = '{{ ngi_containers }}/ampliseq/Silva_132_release.zip' {% endif %} From bcb015a184a2c8e59e3e4e53224abc855c59b503 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Tue, 26 May 2020 16:57:40 +0200 Subject: [PATCH 2/3] Remove superfluous whitespace --- roles/nf-core/tasks/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index af7d1be6..c85c2aaf 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -23,7 +23,7 @@ - name: Create temp directories for singularity images file: - path: "{{ item }}" + path: "{{ item }}" state: directory with_items: - "{{ ngi_containers }}/singularity_cache" From a0a98fe191ac4e91191c02df38b92514fdc63b44 Mon Sep 17 00:00:00 2001 From: Anandashankar Anil Date: Wed, 27 May 2020 11:16:58 +0200 Subject: [PATCH 3/3] Fix typo --- roles/nf-core/tasks/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index c85c2aaf..5754a2b3 100644 --- a/roles/nf-core/tasks/main.yml +++ b/roles/nf-core/tasks/main.yml @@ -81,7 +81,7 @@ - name: Download SILVA classifier data for ampliseq get_url: url: https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip - dest: "{{ ngi_rcontainers }}/ampliseq/Silva_132_release.zip" + dest: "{{ ngi_containers }}/ampliseq/Silva_132_release.zip" - name: Store tool version in deployment lineinfile: