更新 'tasks/arriba.wdl'

--outFileNamePrefix

tasks/arriba.wdl

@@ -22,7 +22,6 @@ task arriba{
             --genomeLoad NoSharedMemory \
             --readFilesIn ${fastq1} ${fastq2} \
             --readFilesCommand zcat \
-            --outStd BAM_Unsorted \
             --outSAMtype BAM Unsorted \
             --outSAMunmapped Within \
             --outBAMcompression 0 \
@@ -37,10 +36,11 @@ task arriba{
             --chimScoreJunctionNonGTAG 0 \
             --chimScoreSeparation 1 \
             --chimSegmentReadGapMax 3 \
-            --chimMultimapNmax 50 > ./output/${sample_id}.Aligned.out.bam
+            --chimMultimapNmax 50 \
+            --outFileNamePrefix ./output/${sample_id}
 
         /arriba_v2.1.0/arriba \
-            -x ./output/${sample_id}.Aligned.out.bam \
+            -x ./output/${sample_id}Aligned.out.bam \
             -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \
             -a ${ASSEMBLY_FA} \
             -g ${ANNOTATION_GTF} \