bug fix

Author: ch99l

.github/workflows/smoke_test.yml

@@ -41,4 +41,4 @@ jobs:
         run: |
           nextflow run . -profile test_base,${{ matrix.profile }},docker \
             ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \
-            ${{ matrix.bam_only && '--bam_only true' || '' }}
+            ${{ matrix.bam_only && '--bam_only' || '' }}

nextflow.config

@@ -57,7 +57,6 @@ profiles {
 
     docker {
         docker.enabled           = true
-        docker.autoMounts        = true
         singularity.enabled      = false
 	    docker.runOptions        = '-u $(id -u):$(id -g)'
     }