Change path input to file for nextflow 0.31.0

astrocyte_pkg.yml

@@ -40,7 +40,6 @@ documentation_files:
 # Specify versioned module names to ensure reproducability.
 workflow_modules:
   - 'singularity/3.0.2'
-  - 'nextflow/19.09.0'
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

workflow/main.nf

@@ -86,7 +86,7 @@ process untarBCL {
   input:
     file untarBCLScript
     file versions_pigzScript
-    each path(tar) from tarList
+    each file(tar) from tarList
 
   output:
     file("*[!version_pigz.txt]") into bclPaths mode flatten
@@ -111,7 +111,7 @@ process mkfastq {
   input:
     file versions_cellrangerScript
     file versions_bcl2fastqScript
-    each path(bcl) from bclPaths.collect()
+    each file(bcl) from bclPaths.collect()
     file design from designPaths
 
   output: