更新 'tasks/arriba.wdl'

/dev/stdin \

tasks/arriba.wdl

@@ -36,11 +36,8 @@ task arriba{
             --chimScoreJunctionNonGTAG 0 \
             --chimScoreSeparation 1 \
             --chimSegmentReadGapMax 3 \
-            --chimMultimapNmax 50 \
-            --outFileNamePrefix ./output/${sample_id}
-
-        /arriba_v2.1.0/arriba \
-            -x ./output/${sample_id}Aligned.out.bam \
+            --chimMultimapNmax 50 |tee ./output/${sample_id}.Aligned.out.bam |/arriba_v2.1.0/arriba \
+            -x /dev/stdin \
             -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \
             -a ${ASSEMBLY_FA} \
             -g ${ANNOTATION_GTF} \