diff --git a/clean.sh b/clean.sh
new file mode 100755
index 0000000000000000000000000000000000000000..da5f9a7fd0b397f846bda15201dec20cfa3ea493
--- /dev/null
+++ b/clean.sh
@@ -0,0 +1,2 @@
+rm -f .nextflow.log*
+rm -rf work/*
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index f183a8751850b73da60b483602e2fc486769274e..7a33655c201b12d88220b9836596f2eadc6e695f 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -70,7 +70,7 @@ if (params.help || params.h) {
  ****************************************************************
 */
  
-params.fastq = "./data/fastq/*_{1,2}.fq*"
+params.fastq = "./data/fastq/*_R{1,2}.fastq.gz"
 params.bam = ""
 params.genome = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.dna.primary_assembly.fa"
 params.gtf = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.87.gtf"
@@ -242,5 +242,5 @@ workflow {
 */
 
   concat_fusion(arriba.out.fusions, arriba.out.discarded)
-  parsefusion(concat_fusion.out.concatenated_fusions)
+  parsefusion(concat_fusion.out.concatenated_fusions, htseq_count.out.counts, design.collect())
 }
\ No newline at end of file