Merge pull request #422 from NationalGenomicsInfrastructure/monthly

Monthly
NationalGenomicsInfrastructure · Jun 28, 2021 · 3242949 · 3242949
2 parents f5b0c03 + 6570aa5
commit 3242949
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Showing 4 changed files with 2 additions and 14 deletions.
diff --git a/host_vars/127.0.0.1/main.yml b/host_vars/127.0.0.1/main.yml
@@ -44,7 +44,7 @@ ngi_pipeline_db_sthlm: "{{ ngi_pipeline_sthlm_path }}/db/records_db_sthlm.sql"
 piper_module_version: 1.5.1
 gatk_bundle_b37: "/sw/data/uppnex/piper_references/2016-04-07/gatk_bundle/2.8/b37/"
 
-sarek_tag: "2.6.1"
+sarek_tag: "2.7"
 sarek_dest: "{{ sw_path }}/sarek"
 sarek_containers: "{{ ngi_containers }}/sarek"
 

diff --git a/roles/archive-upload-ws/defaults/main.yml b/roles/archive-upload-ws/defaults/main.yml
@@ -8,7 +8,7 @@
 # This will set corresponding paths and use the appropriate port.
 
 archive_upload_repo: https://github.com/Molmed/snpseq-archive-upload.git
-archive_upload_version: v1.0.3
+archive_upload_version: v1.0.4
 
 # 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/"

diff --git a/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 b/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2
@@ -33,8 +33,6 @@ ACKNOWLEDGE_SITE="ACKNOWLEDGEMENTS_U.txt"
 fi
 
 ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/DELIVERY.README.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.txt
-ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/scripts/applyRecalibration.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/applyRecalibration.sh
-ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/scripts/bam2fastq.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/bam2fastq.sh
 ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/$ACKNOWLEDGE_SITE {{ proj_root }}/$1/nobackup/NGI/softlinks/ACKNOWLEDGEMENTS.txt
 
 #if sthlm, source delivery readme script

diff --git a/roles/taca/templates/site_taca_delivery.yml.j2 b/roles/taca/templates/site_taca_delivery.yml.j2
@@ -79,12 +79,6 @@ deliver:
         -
             - <ANALYSISPATH>/piper_ngi/03_genotype_concordance/<SAMPLEID>.gt_concordance
             - <STAGINGPATH>/<SAMPLEID>/01-QC
-{% endif %}
-{% if "upps" == site %}
-        -
-            - {{ ngi_site_softlinks }}/bam2fastq.sh
-            - <STAGINGPATH>/<SAMPLEID>/02-FASTQ
-            - required: True
 {% endif %}
         -
             - <ANALYSISPATH>/piper_ngi/05_processed_alignments/<SAMPLEID>.clean.dedup.ba[im]
@@ -94,10 +88,6 @@ deliver:
             - <ANALYSISPATH>/piper_ngi/05_processed_alignments/<SAMPLEID>.pre_recal.table
             - <STAGINGPATH>/<SAMPLEID>/03-BAM
             - required: True
-        -
-            - {{ ngi_site_softlinks }}/applyRecalibration.sh
-            - <STAGINGPATH>/<SAMPLEID>/03-BAM
-            - required: True
         -
             - <ANALYSISPATH>/piper_ngi/07_variant_calls/<SAMPLEID>.clean.dedup.recal.bam.genomic.vcf.gz
             - <STAGINGPATH>/<SAMPLEID>/04-VCF