From 562365f2be5058531d079babe7b481a9d421bc6b Mon Sep 17 00:00:00 2001 From: Sara Sjunnebo Date: Wed, 11 Dec 2024 13:37:17 +0100 Subject: [PATCH 1/3] Bump TACA version --- roles/taca/defaults/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 0a135f3f..b6583239 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -9,7 +9,7 @@ flowcell_parser_version: cfe18abb6b758a6389a9d6aa75f1866d517dc36e taca_repo: https://github.com/SciLifeLab/TACA.git taca_dest: "{{ sw_path }}/TACA" -taca_version: c08d3f3ca4ed2f0f8ef7e669b6d7313b746e33f0 +taca_version: df9915775c4c6c9ed3f9148cc37910bd2d44f37b ngi_pipeline_analysisdir: "{{ ngi_pipeline_workdir }}/ANALYSIS" ngi_pipeline_datadir: "{{ ngi_pipeline_workdir }}/DATA" From c2e640b2e5b038937f9ab5fd05b377bcc4cc7853 Mon Sep 17 00:00:00 2001 From: Sara Sjunnebo Date: Wed, 11 Dec 2024 14:03:26 +0100 Subject: [PATCH 2/3] Add taca config for ONT deliveries --- roles/taca/tasks/main.yml | 1 + .../taca/templates/site_taca_ont_delivery.yml.j2 | 15 +++++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 roles/taca/templates/site_taca_ont_delivery.yml.j2 diff --git a/roles/taca/tasks/main.yml b/roles/taca/tasks/main.yml index fe6aeedb..e6eb61f1 100644 --- a/roles/taca/tasks/main.yml +++ b/roles/taca/tasks/main.yml @@ -44,6 +44,7 @@ - { config_tpl: "taca_cleanup", config_dst: "taca_cleanup", item_type: cleanup, config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_fastq_delivery", item_type: fastq, config_site: ["sthlm"] } - { config_tpl: "taca_runfolder_delivery", config_dst: "taca_runfolder_delivery", item_type: runfolder, config_site: ["sthlm"] } + - { config_tpl: "taca_ont_delivery", config_dst: "taca_ont_delivery", config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_rna_delivery", item_type: rna, config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_denovo_delivery", item_type: denovo, config_site: ["sthlm"] } diff --git a/roles/taca/templates/site_taca_ont_delivery.yml.j2 b/roles/taca/templates/site_taca_ont_delivery.yml.j2 new file mode 100644 index 00000000..983bf6bc --- /dev/null +++ b/roles/taca/templates/site_taca_ont_delivery.yml.j2 @@ -0,0 +1,15 @@ +log: + file: "{{ ngi_pipeline_path }}/log/taca.log" + +organise: + incoming_path: "{{ proj_root }}/{{ uppmax_project }}/incoming" + nanopore_path: "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/ONT_TAR" + illumina_path: "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/DATA" + element_path: "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/DATA" + +delivery: + data_locations: + - "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/ONT_TAR" + - "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/DATA" + - "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/ANALYSIS" + staging_path: "{{ proj_root }}/{{ uppmax_project }}/nobackup/NGI/DELIVERY" From ef5f693d7aaba45c64070775a17d54b552a3a61d Mon Sep 17 00:00:00 2001 From: Sara Sjunnebo Date: Mon, 16 Dec 2024 08:31:01 +0100 Subject: [PATCH 3/3] Rename new config for TACA --- roles/taca/tasks/main.yml | 2 +- ...nt_delivery.yml.j2 => site_taca_organise_and_deliver.yml.j2} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename roles/taca/templates/{site_taca_ont_delivery.yml.j2 => site_taca_organise_and_deliver.yml.j2} (100%) diff --git a/roles/taca/tasks/main.yml b/roles/taca/tasks/main.yml index e6eb61f1..14c19f18 100644 --- a/roles/taca/tasks/main.yml +++ b/roles/taca/tasks/main.yml @@ -44,7 +44,7 @@ - { config_tpl: "taca_cleanup", config_dst: "taca_cleanup", item_type: cleanup, config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_fastq_delivery", item_type: fastq, config_site: ["sthlm"] } - { config_tpl: "taca_runfolder_delivery", config_dst: "taca_runfolder_delivery", item_type: runfolder, config_site: ["sthlm"] } - - { config_tpl: "taca_ont_delivery", config_dst: "taca_ont_delivery", config_site: ["sthlm"] } + - { config_tpl: "taca_organise_and_deliver", config_dst: "taca_organise_and_deliver", config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_rna_delivery", item_type: rna, config_site: ["sthlm"] } - { config_tpl: "app_specific_delivery", config_dst: "taca_denovo_delivery", item_type: denovo, config_site: ["sthlm"] } diff --git a/roles/taca/templates/site_taca_ont_delivery.yml.j2 b/roles/taca/templates/site_taca_organise_and_deliver.yml.j2 similarity index 100% rename from roles/taca/templates/site_taca_ont_delivery.yml.j2 rename to roles/taca/templates/site_taca_organise_and_deliver.yml.j2