Merge pull request #8 from johanherman/inject-siswrap-confs

Fetch conf from Hermes and inject into Siswrap

actions/parse_siswrap_args.yaml

@@ -0,0 +1,22 @@
+---
+name: parse_siswrap_args
+runner_type: python-script
+description: Parses siswrap args to json
+enabled: true
+entry_point: lib/parse_arguments_to_json.py
+parameters:
+
+  sisyphus_conf:
+    default: ""
+    type: string
+    description: "String containing the entire config file for Sisyphus (not just a path to it)."
+
+  qc_conf:
+    default: ""
+    type: string
+    description: "String containing the entire QC criteria config file (not just a path to it)."
+
+  runfolder:
+    default: ""
+    type: string
+    description: "Name of the runfolder to process"

actions/workflows/ngi_uu_workflow.yaml

@@ -102,18 +102,37 @@ workflows:
                 input:
                     url: <% $.bcl2fastq_status_url %>
                 on-success:
-                    - run_sisyphus_quick_report
+                    - download_sisyphus_config
             ### DEMULTIPLEX END ###
 
-
             ### QUICK REPORT START ###
+            download_sisyphus_config:
+                action: core.http
+                input:
+                    url: <% $.hermes_base_url %>/<% $.flowcell_name %>/configfile
+                    headers: USER=<% $.hermes_user %>&X-XSRF-TOKEN=<% $.hermes_token %>
+                publish:
+                    sisyphus_conf_string: <% $.download_sisyphus_config.body.config %>
+                on-success:
+                    - construct_report_body
+
+            construct_report_body:
+                action: arteria-packs.parse_siswrap_args
+                input:
+                    runfolder: "<% $.runfolder_name %>"
+                    sisyphus_conf: "<% $.sisyphus_conf_string %>"
+                publish:
+                    report_body: <% $.construct_report_body.stdout %>
+                on-success:
+                    - run_sisyphus_quick_report
+
             run_sisyphus_quick_report:
                 action: core.http
                 input:
                     url: "http://<% $.host %>:<% $.siswrap_service_port %>/api/1.0/report/run/<% $.runfolder_name %>"
                     method: "POST"
                     headers: "Content-Type=application/json"
-                    body: '{"runfolder": "<% $.runfolder_name %>"}'
+                    body: <% $.report_body %>
                 publish:
                     report_status_url: "<% $.run_sisyphus_quick_report.body.link %>"
                 on-success:
@@ -124,17 +143,37 @@ workflows:
                 input:
                     url: "<% $.report_status_url %>"
                 on-success:
-                    - run_sisyphus_qc
+                    - download_qc_config
             ### QUICK REPORT END ###
 
             ### QUALITY CONTROL START ###
+            download_qc_config:
+                action: core.http
+                input:
+                    url: <% $.hermes_base_url %>/<% $.flowcell_name %>/qcfile
+                    headers: USER=<% $.hermes_user %>&X-XSRF-TOKEN=<% $.hermes_token %>
+                publish:
+                    qc_conf_string: <% $.download_qc_config.body.qc %>
+                on-success:
+                    - construct_qc_body
+
+            construct_qc_body:
+                action: arteria-packs.parse_siswrap_args
+                input:
+                    runfolder: "<% $.runfolder_name %>"
+                    qc_conf: "<% $.qc_conf_string %>"
+                publish:
+                    qc_body: <% $.construct_qc_body.stdout %>
+                on-success:
+                    - run_sisyphus_qc
+
             run_sisyphus_qc:
                 action: core.http
                 input:
                     url: "http://<% $.host %>:<% $.siswrap_service_port %>/api/1.0/qc/run/<% $.runfolder_name %>"
                     method: "POST"
                     headers: "Content-Type=application/json"
-                    body: '{"runfolder": "<% $.runfolder_name %>"}'
+                    body: <% $.qc_body %>
                 publish:
                     qc_status_url: "<% $.run_sisyphus_qc.body.link %>"
                 on-success:
@@ -200,4 +239,4 @@ workflows:
                     body: "An oh shit error occurred while processing <% $.runfolder_name %> on host <% $.host %>. Please investigate!"
                 on-complete:
                   - fail
-                  ### NOTIFIER END ###
+            ### NOTIFIER END ###