Merge pull request #4 from c3g/freezeman_finalSync

Freezeman final sync
c3g · Jan 7, 2025 · 325f853 · 325f853
2 parents 6be71e8 + f128b64
commit 325f853
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Showing 3 changed files with 12 additions and 6 deletions.
diff --git a/assets/email_run_finish.groovy b/assets/email_run_finish.groovy
@@ -40,7 +40,7 @@ html(lang:'en') {
     body {
         div(style:"font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 900px; margin: 0 auto;") {
             h3 "Run: ${event.data.run_name} (${run.flowcell})"
-            h3 "Folder: ${run.analysis_dir}"
+            h3 "Folder: [${run.analysis_dir}]"
             p {
                 span "Run processing finished. Full report attached to this email, but also available "
                 a ( href:"https://datahub-297-p25.p.genap.ca/Freezeman_validation/${event.year}/${event.data.run_name}.report.html", "on GenAP" )

diff --git a/lib/MultiQC.groovy b/lib/MultiQC.groovy
@@ -13,7 +13,7 @@ class MultiQC {
         def file = new File(path)
         def jsonSlurper = new JsonSlurper().setType( JsonParserType.LAX )
         this.data = jsonSlurper.parseText(file.text)
-        this.analysis_dir = data?.config_analysis_dir
+        this.analysis_dir = data?.config_analysis_dir[0]
         def config_report_header_info = data?.config_report_header_info
         this.flowcell = config_report_header_info.find { it.containsKey("Flowcell") }.Flowcell
         this.run = config_report_header_info.find { it.containsKey("Run") }.Run
@@ -22,7 +22,7 @@ class MultiQC {
     MultiQC(Path path) {
         def jsonSlurper = new JsonSlurper().setType( JsonParserType.LAX )
         this.data = jsonSlurper.parseText(path.getText())
-        this.analysis_dir = data?.config_analysis_dir
+        this.analysis_dir = data?.config_analysis_dir[0]
         def config_report_header_info = data?.config_report_header_info
         this.flowcell = config_report_header_info.find { it.containsKey("Flowcell") }.Flowcell
         this.run = config_report_header_info.find { it.containsKey("Run") }.Run

diff --git a/workflows/freezeman/monitor.nf b/workflows/freezeman/monitor.nf
@@ -73,11 +73,17 @@ process FinalSync {
     tuple val(multiqc_html), val(multiqc) 
 
     script:
-    def run_dir = multiqc.analysis_dir.toString()
+    def rundir = multiqc.analysis_dir
+    def db = new MetadataDB(params.db, log)
+    def runinf = db.latestRunInfofile(multiqc.flowcell)
 
     """
-    rundir=\$( echo $run_dir | sed 's/\\[//' | sed 's/\\]//' )
-    rsync -av /nb/Research/freezeman-processing/${multiqc.seqtype}/*/\${rundir}/report/multiqc_* /lb/robot/research/freezeman-processing/${multiqc.seqtype}/*/\${rundir}/report
+    rsync -av /nb/Research/freezeman-processing/${multiqc.seqtype}/${runinf.year}/${rundir}/report/multiqc_* \\
+        /lb/robot/research/freezeman-processing/${multiqc.seqtype}/${runinf.year}/${rundir}/report
+    curl -k -X POST https://dashrunr.c3g-app.sd4h.ca/update \\
+        -H "descrambler-key: \$(cat ~/assets/run-processing-update-headers)" \\
+        -H "Content-Type: application/json" \\
+        -d @/nb/Research/freezeman-processing/${multiqc.seqtype}/${runinf.year}/${rundir}/report/multiqc_data/multiqc_data.json
     """
 }