Add ability to adjust AUGUR_RECURSION_LIMIT env var

main.nf

@@ -33,6 +33,7 @@ Optional arguments:
  --lat_long                     Sample latitudes and longitudes [./config/lat_longs.csv]
  --auspice                      Specifications for visualization in auspice (ex. title) [./config/auspice_config.json]
  --divergence_units             Units used to measure divergence in phylogeny refining step [mutations]
+ --recursion_limit              Augur recursion threshold used to set env variable [10000]
  --conda_cache                  File system path where Conda env is to be stored [fluflo-main/work/]
  --version                      Current fluflo version number
  --help                         This usage statement
@@ -194,6 +195,8 @@ process export {
   file("flu_na.json")
 
       """
+      export AUGUR_RECURSION_LIMIT=${params.recursion_limit}
+
       augur export v2 \
           --tree ${refine_tree} \
           --metadata ${params.meta} \

nextflow.config

@@ -4,7 +4,7 @@ manifest {
   homePage = 'https://github.com/j3551ca/fluflo'
   description = 'Phylogenetics in Nextflow'
   mainScript = 'main.nf'
-  version = '0.1.2'
+  version = '0.1.3'
 }
 
 //pipeline parameters
@@ -47,6 +47,9 @@ auspice = "${params.work_dir}config/auspice_config.json"
 //refining phylogeny
 divergence_units = "mutations"
 
+//env variable AUGUR_RECURSION_LIMIT
+recursion_limit = 10000
+
 }
 
 //seamlessly run pipeline on different execution systems by modifying