Fix issue with empty params initialising to booleans

- Tested with bpipe v0.9.12
- Empty params, e.g., `-p assemblyFasta` are now initialised to
  a boolean value and thus fail the empty string test, need to
  remove these params from params.txt (if not using them)
- Need to set var_filter and gene_filter params if missing
  binding

Author: mcmero

MINTIE.groovy

@@ -30,6 +30,12 @@ if(!binding.variables.containsKey("run_de_step")){
 if(!binding.variables.containsKey("splice_motif_mismatch")){
     splice_motif_mismatch=0
 }
+if(!binding.variables.containsKey("var_filter")){
+    var_filter=""
+}
+if(!binding.variables.containsKey("gene_filter")){
+    gene_filter=""
+}
 
 fastq_dedupe = {
     from("*.gz"){

MINTIE_SE.groovy

@@ -30,6 +30,12 @@ if(!binding.variables.containsKey("run_de_step")){
 if(!binding.variables.containsKey("splice_motif_mismatch")){
     splice_motif_mismatch=0
 }
+if(!binding.variables.containsKey("var_filter")){
+    var_filter=""
+}
+if(!binding.variables.containsKey("gene_filter")){
+    gene_filter=""
+}
 
 fastq_dedupe = {
     from("*.gz"){

test/test_params.txt

@@ -13,10 +13,7 @@
 -p min_cpm=0.1
 -p fdr=0.05
 -p sort_ram=2G
--p gene_filter=
--p var_filter=
 -p splice_motif_mismatch=4
 -p fastqCaseFormat=cases/%_R*.fastq.gz
 -p fastqControlFormat=controls/%_R*.fastq.gz
--p assemblyFasta=
 -p run_de_step=true