Merge pull request #419 from NationalGenomicsInfrastructure/monthly

Production deployment May 2021

roles/archive-upload-ws/defaults/main.yml

@@ -1,14 +1,14 @@
 ---
 
-# If deploying to staging one should call with 
+# If deploying to staging one should call with
 # -e deployment_environment=staging
-# One can also override the default installed version 
-# by overriding the archive_upload_version on the command line. 
+# One can also override the default installed version
+# by overriding the archive_upload_version on the command line.
 #
-# This will set corresponding paths and use the appropriate port.  
+# This will set corresponding paths and use the appropriate port.
 
 archive_upload_repo: https://github.com/Molmed/snpseq-archive-upload.git
-archive_upload_version: v1.0.2
+archive_upload_version: v1.0.3
 
 # in production this should be  /proj/ngi2016001/nobackup/NGI/ANALYSIS/<PROJECT ID>
 archive_upload_monitored_path_prod: "/proj/{{ ngi_pipeline_upps_delivery }}/nobackup/NGI/ANALYSIS/"
@@ -27,11 +27,11 @@ archive_upload_logger_config: "{{ archive_upload_config_root }}/logger.config"
 archive_upload_log_dir: "/proj/{{ ngi_pipeline_upps_delivery }}/private/log/arteria/archive-upload-ws"
 
 archive_upload_port_prod: 10480
-archive_upload_port_stage: 10481 
+archive_upload_port_stage: 10481
 archive_upload_cores_to_use: 2
 
 # We want to fake a successful return code for the dsmc subprocess for some certain warnings.
-# Otherwise the Arteria workflow in Stackstorm would be marked as failed when it actually suceeded.  
+# Otherwise the Arteria workflow in Stackstorm would be marked as failed when it actually suceeded.
 #
 # ANS1809W = a session with the TSM server has been disconnected: will retry again
 # ANS2042W = a symblic link to a file on other fs has been uploaded: acls/extended attributes might not be backed up

roles/multiqc/defaults/main.yml

@@ -1,6 +1,6 @@
 multiqc_repo: https://github.com/ewels/MultiQC.git
 multiqc_dest: "{{ sw_path }}/multiqc"
-multiqc_version: "v1.10"
+multiqc_version: "v1.10.1"
 
 multiqc_ngi_repo: https://github.com/NationalGenomicsInfrastructure/MultiQC_NGI.git
 multiqc_ngi_dest: "{{ sw_path }}/multiqc_ngi"

roles/nf-core/defaults/main.yml

@@ -4,11 +4,11 @@ nextflow_download_url: "https://github.com/nextflow-io/nextflow/releases/downloa
 nf_core_env: "/lupus/ngi/irma3/nf-core-env"
 pipelines:
   - name: methylseq
-    release: 1.6
+    release: 1.6.1
   - name: ampliseq
-    release: 1.1.2
+    release: 1.2.0
   - name: atacseq
-    release: 1.1.0
+    release: 1.2.1
   - name: viralrecon
     release: 1.1.0
   - name: rnafusion

roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2

@@ -39,5 +39,5 @@ ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/$ACKNOWLEDG
 
 #if sthlm, source delivery readme script
 if [ $1 == "ngi2016003" ]; then
-. create_delivery_readme_softlinks.sh
+. {{ ngi_resources }}/create_delivery_readme_softlinks.sh
 fi

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: 1d7ca548099ed3b08dd33fff59f6b8652b323707
+taca_ngi_version: 79d6f1b38dd5808b0ab4a3e7a732c989e5cc7ec1
 
 statusdb_repo: "https://github.com/SciLifeLab/statusdb.git"
 statusdb_dest: "{{ sw_path }}/statusdb"

roles/taca/templates/create_delivery_readme_softlinks.sh.j2

@@ -16,4 +16,4 @@ fi
 ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.RAW_DATA.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.RAW_DATA.txt
 ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.MethylSeq.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.MethylSeq.txt
 ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.RNASeq.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.RNASeq.txt
-ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.Sarek.txt {{ ngi_resources }}/TACA/sthlm/DELIVERY.README.SAREK.txt
+ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.Sarek.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.SAREK.txt

roles/taca/templates/site_taca_sarek_delivery.yml.j2

@@ -7,8 +7,8 @@ deliver:
     stagingpath: <ROOTPATH>/DELIVERY/<PROJECTID>
     operator: "{{ recipient_mail }}"
     hash_algorithm: md5
-    files_to_deliver:
 {% if "upps" == site %}
+    files_to_deliver:
         -
             - <ANALYSISPATH>/seqreports/*
             - <STAGINGPATH>/00-Reports/SequenceQC/
@@ -21,17 +21,6 @@ deliver:
             - <ANALYSISPATH>/multiqc_ngi/*multiqc_report_data.zip
             - <STAGINGPATH>/00-Reports/
             - required: True
-{% endif %}
-{% if "sthlm" == site %}
-        -
-            - <ANALYSISPATH>/sarek_ngi/*multiqc_report.html
-            - <STAGINGPATH>/00-Reports/
-            - required: True
-        -
-            - <ANALYSISPATH>/reports/*
-            - <STAGINGPATH>/00-Reports/
-            - required: True
-{% endif %}
         -
             - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Annotation/*
             - <STAGINGPATH>/<SAMPLEID>/results/Annotation/
@@ -68,3 +57,59 @@ deliver:
             - {{ ngi_resources }}/TACA/apply_recalibration.sh
             - <STAGINGPATH>/01-Resources/
             - required: True
+{% endif %}
+{% if "sthlm" == site %}
+    datapath: <ROOTPATH>/DATA/<PROJECTID>
+    stagingpathhard: <ROOTPATH>/DELIVERY_HARD/<PROJECTID>
+    files_to_deliver:
+        -
+            - <DATAPATH>/<SAMPLEID>/*/*
+            - <STAGINGPATH>/<SAMPLEID>/02-FASTQ
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Annotation/*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/Annotation/
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/pipeline_info/results_description.html
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/pipeline_info
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/pipeline_info/software_versions.csv
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/pipeline_info
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Preprocessing/TSV/duplicates_marked*<SAMPLEID>.tsv*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/Preprocessing/TSV
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Preprocessing/<SAMPLEID>/DuplicatesMarked/*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/Preprocessing/DuplicatesMarked
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Preprocessing/<SAMPLEID>/Recalibrated/*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/Preprocessing/Recalibrated
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/Reports/*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/Reports
+            - required: True
+        -
+            - <ANALYSISPATH>/<SAMPLEID>/SarekGermlineAnalysis/results/VariantCalling/<SAMPLEID>/*
+            - <STAGINGPATH>/<SAMPLEID>/01-SarekGermline-Results/VariantCalling/
+            - required: True
+    misc_files_to_deliver:
+        -
+            - {{ ngi_site_softlinks }}/ACKNOWLEDGEMENTS.txt
+            - <STAGINGPATH>
+        -
+            - {{ ngi_site_softlinks }}/DELIVERY.README.SAREK.txt
+            - <STAGINGPATH>
+        -
+            - <ANALYSISPATH>/reports/*
+            - <STAGINGPATH>/00-Reports
+        -
+            - <ANALYSISPATH>/*multiqc_report.html
+            - <STAGINGPATH>/00-Reports
+    save_meta_info: True
+{% endif %}