Merge pull request #296 from ssjunnebo/bimonthly

Update TACA version and add config file
NationalGenomicsInfrastructure · Dec 16, 2024 · cf7d395 · cf7d395
2 parents 432d5e6 + ef5f693
commit cf7d395
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diff --git 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"

diff --git 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_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_organise_and_deliver.yml.j2 b/roles/taca/templates/site_taca_organise_and_deliver.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"