Fix bug, is empty

workflow/main.nf

@@ -23,9 +23,13 @@ indel="$params.genome/GoldIndels.vcf.gz"
 knownindel=file(indel)
 dbsnp=file(dbsnp)
 
-repoDir=workflow.projectDir
+
 if (params.repoDir) {
-   repoDir=params.repoDir
+  repoDir=params.repoDir
+} else if (workflow.projectDir) {
+  repoDir=workflow.projectDir
+} else {
+  repoDir="$baseDir"
 }
 
 // params genome is the directory
@@ -90,12 +94,15 @@ process ralign {
   errorStrategy 'ignore'
   label 'ralign'
   publishDir "$params.output", mode: 'copy'
+  
   input:
   set pair_id, file(fqs) from trimread
+  
   output:
   set pair_id, file("${pair_id}.bam") into aligned
   set pair_id, file("${pair_id}.bam") into aligned2
   file("${pair_id}.alignerout.txt") into hsatout
+  
   script:
   """
   bash $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}