From 8161dc6e6413581e769ea0cddfaeb0234c769ae8 Mon Sep 17 00:00:00 2001
From: Isak Sylvin <isak.sylvin@scilifelab.se>
Date: Tue, 11 Oct 2016 11:41:13 +0200
Subject: [PATCH 1/4] Added test cores for staging

---
 roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
index 054904f2..dc3e69cb 100644
--- a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
+++ b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
@@ -14,7 +14,11 @@ environment:
             - {{ proj_root }}/{{ ngi_pipeline_upps_delivery }}/incoming
 # TODO: This QOS flag is probably not used/needed any longer. 
 #       Enable later in the future if required. 
-#slurm:
+slurm:
+{% if "{{ deployment_environment }}" == [ "staging", "devel" ] %}
+     queue: 
+         - devcore
+{% endif } 
 #    extra_params:
 #        "--qos": "seqver"
 piper:

From 67fb697aeb30f2fe33f725d0a5619f4897a11a33 Mon Sep 17 00:00:00 2001
From: Isak Sylvin <isak.sylvin@scilifelab.se>
Date: Tue, 11 Oct 2016 11:43:37 +0200
Subject: [PATCH 2/4] Minor ngi_pipeline config syntax error

---
 roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
index dc3e69cb..aa40510b 100644
--- a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
+++ b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
@@ -14,13 +14,13 @@ environment:
             - {{ proj_root }}/{{ ngi_pipeline_upps_delivery }}/incoming
 # TODO: This QOS flag is probably not used/needed any longer. 
 #       Enable later in the future if required. 
-slurm:
+
 {% if "{{ deployment_environment }}" == [ "staging", "devel" ] %}
+slurm:
      queue: 
          - devcore
-{% endif } 
-#    extra_params:
-#        "--qos": "seqver"
+{% endif }
+ 
 piper:
     #sample:
     #    required_autosomal_coverage: 28.4

From 87d9d4561aa0f75c7aa22aaabe693fd0137dbc2b Mon Sep 17 00:00:00 2001
From: sylvinite <i.sylvin@null.net>
Date: Tue, 11 Oct 2016 16:19:34 +0200
Subject: [PATCH 3/4] Fixed multiqc conf and test cores conf

---
 roles/multiqc/templates/multiqc_config.yml.j2        | 2 +-
 roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/roles/multiqc/templates/multiqc_config.yml.j2 b/roles/multiqc/templates/multiqc_config.yml.j2
index b62d08f6..efaa3626 100644
--- a/roles/multiqc/templates/multiqc_config.yml.j2
+++ b/roles/multiqc/templates/multiqc_config.yml.j2
@@ -14,7 +14,7 @@ fn_ignore_paths:
     - '*/piper_ngi/04_merged_alignments/*'
 
 #True for production, False for Staging
-{% if "{{ deployment_environment }}" == "production" %}
+{% if deployment_environment == "production" %}
 push_statusdb: True
 save_remote: True
 remote_sshkey: '~/.ssh/id_rsa'  # Optional
diff --git a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2 b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
index aa40510b..901280ee 100644
--- a/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
+++ b/roles/ngi_pipeline/templates/irma_ngi_config.yaml.j2
@@ -15,11 +15,11 @@ environment:
 # TODO: This QOS flag is probably not used/needed any longer. 
 #       Enable later in the future if required. 
 
-{% if "{{ deployment_environment }}" == [ "staging", "devel" ] %}
+{% if deployment_environment in [ "staging", "devel" ] %}
 slurm:
      queue: 
          - devcore
-{% endif }
+{% endif %}
  
 piper:
     #sample:

From 826f5ebba1d73f5bdda633eab653957eb48df944 Mon Sep 17 00:00:00 2001
From: sylvinite <i.sylvin@null.net>
Date: Tue, 11 Oct 2016 16:56:26 +0200
Subject: [PATCH 4/4] Restricted multiqc conf parts to sthlm

---
 roles/multiqc/templates/multiqc_config.yml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/roles/multiqc/templates/multiqc_config.yml.j2 b/roles/multiqc/templates/multiqc_config.yml.j2
index efaa3626..138ac70e 100644
--- a/roles/multiqc/templates/multiqc_config.yml.j2
+++ b/roles/multiqc/templates/multiqc_config.yml.j2
@@ -14,7 +14,7 @@ fn_ignore_paths:
     - '*/piper_ngi/04_merged_alignments/*'
 
 #True for production, False for Staging
-{% if deployment_environment == "production" %}
+{% if deployment_environment == "production" and item.site == "sthlm" %}
 push_statusdb: True
 save_remote: True
 remote_sshkey: '~/.ssh/id_rsa'  # Optional