updated nextflow.config

Author: jpalmer37

nextflow.config

@@ -14,7 +14,7 @@ params {
   fasta_exts = ['*.fa', '*.fasta', '*.fna']
   fasta_search_path = makeFastaSearchPath(fasta_exts)
   fasta_input = 'NO_FILE'
-  run_name = "default"
+  run_name = parseRunName( fasta_input )
   samplesheet_input = 'NO_FILE'
   databases = 'NO_FILE'
   no_db_metadata = false
@@ -35,6 +35,16 @@ def makeFastaSearchPath (fasta_exts) {
     return fasta_search_path
 }
 
+// this uses a regex invocation using the =~ to pull out the folder name
+def parseRunName ( fasta_input ) {
+    run_name = (params.fasta_input =~ /([^\/]+)\/?$/)[0][1]
+    if (!run_name) {                                                         
+      throw new RuntimeException("ERROR: Parsing run name from FASTQ path failed.")
+    }
+    return run_name
+}
+
+
 def parseMinorVersion(version) {
     minor_version = version.split('\\.')[0..1].join('.')
     return minor_version
@@ -59,5 +69,19 @@ process {
   withName: blastn {
     shell = ['/bin/bash', '-uo','pipefail' ]
   }
+}
+
+report {
+    enabled = true
+    file = "${params.outdir}/${params.run_name}_its-nf_nextflow_report.html"
+}
+
+timeline {
+    enabled = true
+    file = "${params.outdir}/${params.run_name}_its-nf_nextflow_timeline.html"
+}
 
+trace {
+    enabled = true
+    file = "${params.outdir}/${params.run_name}_its-nf_nextflow_trace.txt"
 }