Try accessing secrets in the module?

nf-core · Jul 15, 2024 · 62dd7e7 · 62dd7e7
1 parent 2d969a4
commit 62dd7e7
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
@@ -33,9 +33,9 @@ process SENTIEON_BWAMEM {
 
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? secrets.SENTIEON_LICENSE_BASE64 : ""
     """
-    if [ -n "\${SENTIEON_LICENSE_BASE64}" ]; then
+    if [ -n $sentieonLicense ]; then
         # NOTE: This is how pipeline users will test out Sentieon
         echo "Localhost license file"
         # The license file is stored as a nextflow variable like, for instance, this:

diff --git a/modules/nf-core/sentieon/bwamem/tests/nextflow.config b/modules/nf-core/sentieon/bwamem/tests/nextflow.config
@@ -5,7 +5,7 @@ env {
     SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH"
     SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
     // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
-    // SENTIEON_LICENSE_BASE64 = secrets.SENTIEON_LICENSE_BASE64
+    // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
 }
 
 process {