Merge pull request #4 from blue-moon22/dev

Dev
blue-moon22 · Jul 24, 2023 · d85894e · d85894e
2 parents e3d91ae + c9da205
commit d85894e
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diff --git a/README.md b/README.md
@@ -54,6 +54,8 @@ Note: You may be warned to first call `git config --global --add safe.directory`
 nextflow palidis.nf --manifest <manifest_file> --batch_name <batch_name> -c configs/conf/<name_of_config>.config
 ```
 
+If you are using a cluster and it uses singularity instead of docker, please add `-profile standard,singularity`
+
 ### Mandatory arguments
 #### `<batch_name>`
 

diff --git a/nextflow.config b/nextflow.config
@@ -24,9 +24,6 @@ params {
 profiles {
 
         standard {
-                docker {
-                        enabled = true
-                }
                 process {
                         container = 'bluemoon222/palidis_dependencies:0.0.22'
                         cpus = 1
@@ -145,4 +142,11 @@ profiles {
                         }
                 }
         }
+        singularity {
+                singularity {
+                        enabled = true
+                        autoMounts = true
+                        cacheDir = "$projectDir/singularity"
+                }
+        }
 }