BSJ files are in BSJ subfolder

Author: kopardev

workflow/Snakefile

@@ -163,13 +163,13 @@ rule all:
 		expand(join(WORKDIR,"results","{sample}","customBSJs","{sample}.valid_STAR_BSJ.bed"),sample=SAMPLES),
 		expand(join(WORKDIR,"results","{sample}","customBSJs","{sample}.novel_CIRI_BSJ.bed"),sample=SAMPLES),
 		expand(join(WORKDIR,"results","{sample}","customBSJs","{sample}.BSJ.bed"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.bam"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.bw"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.plus.bam"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.plus.bw"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.minus.bam"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.minus.bw"),sample=SAMPLES),
-		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.BSJ.hg38.bed"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.bam"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.bw"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.plus.bam"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.plus.bw"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.minus.bam"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.minus.bw"),sample=SAMPLES),
+		expand(join(WORKDIR,"results","{sample}","STAR2p","BSJs","{sample}.BSJ.hg38.bed"),sample=SAMPLES),
 		## Spliced reads bams and bigwigs
 		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.spliced_reads.hg38.bam"),sample=SAMPLES),
 		expand(join(WORKDIR,"results","{sample}","STAR2p","{sample}.spliced_reads.hg38.bw"),sample=SAMPLES),