10x org_yaml

Author: katsikora

BRB/PushButton.py

@@ -445,7 +445,11 @@ def scRNAseq(config, group, project, organism, libraryType, tuples):
         'Chromium_NextGEM_SingleCell3Prime_GeneExpression_v3.1_DualIndex',
         'Chromium_GEM-X_SingleCell_3primeRNA-seq_v4'
     ]
+
+
     if tuples[0][2] in accepted_names:
+        if 'GRCh38' in org_yaml:
+            org_yaml = 'GRCh38'
         PE = linkFiles(config, group, project, outputDir, tuples)
         CMD = [config.get('10x', 'RNA'), outputDir, outputDir, org_yaml]
         log.info(f"scRNA wf CMD: {' '.join(CMD)}")

eval "$(ssh-agent -s)"

@@ -0,0 +1,7 @@
+-----BEGIN OPENSSH PRIVATE KEY-----
+b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW
+QyNTUxOQAAACCe87DFQk05SeB/i9vpEbUlPze85bCmQj2RMMiMo1sN3wAAAKBhnmRXYZ5k
+VwAAAAtzc2gtZWQyNTUxOQAAACCe87DFQk05SeB/i9vpEbUlPze85bCmQj2RMMiMo1sN3w
+AAAEBDzOC6QO7vwPRVjHIjx3h4RSqP/VtM8ZT9BwNGEFQM0J7zsMVCTTlJ4H+L2+kRtSU/
+N7zlsKZCPZEwyIyjWw3fAAAAGXNpa29yYUBpZS1mcmVpYnVyZy5tcGcuZGUBAgME
+-----END OPENSSH PRIVATE KEY-----

eval "$(ssh-agent -s)".pub

@@ -0,0 +1 @@
+ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIJ7zsMVCTTlJ4H+L2+kRtSU/N7zlsKZCPZEwyIyjWw3f [email protected]