Accomodate different header fields

Author: grosscol

workflows/eqtl/eqtl.nf

@@ -69,6 +69,8 @@ process merge_files {
   input:
   file file_list
   val analysis_type
+  val fields
+  val types
 
   output:
   file "all.${analysis_type}.tsv"
@@ -77,7 +79,7 @@ process merge_files {
 
   script:
   outfile = "all.${analysis_type}.tsv"
-  mongo_hdr = GroovyCollections.transpose( params.cond_fields, params.cond_types)
+  mongo_hdr = GroovyCollections.transpose( fields, types)
                 .collect{arr -> arr.join(".") + "()"}
                 .plus("tissue.string()")
                 .join("\t")
@@ -93,23 +95,27 @@ process merge_files {
 }
 
 workflow conditional_eqtl {
+  analysis_type = "cond"
   cond_tsv      = channel.fromPath("${params.cond_eqtl_glob}")
   cond_headers  = channel.of(params.cond_fields).collect()
-  analysis_type = "cond"
+  fields        = params.cond_fields
+  types         = params.cond_types
 
   validate_header(cond_tsv, cond_headers)
   munge_files(cond_tsv, analysis_type)
-  merge_files(munge_files.out.collect(), analysis_type)
+  merge_files(munge_files.out.collect(), analysis_type, fields, types)
 }
 
 workflow susie_eqtl {
+  analysis_type = "susie"
   susie_tsv     = channel.fromPath("${params.susie_eqtl_glob}")
   susie_headers = channel.of(params.susie_fields).collect()
-  analysis_type = "susie"
+  fields        = params.susie_fields
+  types         = params.susie_types
 
   validate_header(susie_tsv, susie_headers)
   munge_files(susie_tsv, analysis_type)
-  merge_files(munge_files.out.collect(), analysis_type)
+  merge_files(munge_files.out.collect(), analysis_type, fields, types)
 }
 
 workflow {