fix: Spike in with environment variables

nf-core · Jul 2, 2024 · b90654c · b90654c
1 parent 41a1305
commit b90654c
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
@@ -10,7 +10,7 @@ process SENTIEON_BWAMEM {
     // If they use a public license server
     // secret 'SENTIEON_ENCRYPTION_KEY' // NOTE Only actual secret
     // secret 'SENTIEON_LICENSE_MESSAGE'
-    secret 'SENTIEON_AUTH_MECH'
+    // secret 'SENTIEON_AUTH_MECH'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

diff --git a/modules/nf-core/sentieon/bwamem/tests/nextflow.config b/modules/nf-core/sentieon/bwamem/tests/nextflow.config
@@ -1,10 +1,13 @@
+env {
+    SENTIEON_LICSRVR_IP="$SENTIEON_LICSRVR_IP"
+    SENTIEON_AUTH_MECH="$SENTIEON_AUTH_MECH"
+}
+
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: 'SENTIEON_BWAMEM' {
-        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
-        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
         ext.args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\""
     }