更新 'tasks/arriba.wdl'

Array[File] arriba_pdf=glob("./output/*.pdf")

tasks/arriba.wdl

@@ -22,7 +22,7 @@ task arriba{
             --genomeLoad NoSharedMemory \
             --readFilesIn ${fastq1} ${fastq2} \
             --readFilesCommand zcat \
-            --outSAMtype BAM Unsorted \
+            --outSAMtype BAM SortedByCoordinate \
             --outSAMunmapped Within \
             --outBAMcompression 0 \
             --outFilterMultimapNmax 50 \
@@ -41,7 +41,7 @@ task arriba{
                   
                   
          /arriba_v2.1.0/arriba \
-            -x ./output/${sample_id}.Aligned.out.bam \
+            -x ./output/${sample_id}.Aligned.sortedByCoord.out.bam \
             -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \
             -a ${ASSEMBLY_FA} \
             -g ${ANNOTATION_GTF} \
@@ -49,6 +49,17 @@ task arriba{
             -k /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
             -t /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
             -p /arriba_v2.1.0/database/protein_domains_hg38_GRCh38_v2.1.0.gff3
+         
+         samtools index -@ 16 ./output/${sample_id}.Aligned.sortedByCoord.out.bam ./output/${sample_id}.Aligned.sortedByCoord.out.bam.bai
+         
+         Rscript /arriba_v2.1.0/draw_fusions.R \
+            --fusions=./output/${sample_id}_fusions.tsv \
+            --alignments=./output/${sample_id}.Aligned.sortedByCoord.out.bam \
+            --output=./output/${sample_id}_fusion.pdf \
+            --annotation=${ANNOTATION_GTF} \
+            --cytobands=/arriba_v2.1.0/database/cytobands_hg38_GRCh38_v2.1.0.tsv \
+            --proteinDomains=/arriba_v2.1.0/database/protein_domains_hg38_GRCh38_v2.1.0.gff3
+
 
 
     >>>
@@ -62,7 +73,8 @@ task arriba{
 
     output {
         Array[File] arriba_result=glob("./output/*.tsv")
-        Array[File] arriba_bam=glob("./output/*.bam")
+        Array[File] arriba_bam=glob("./output/*.bam*")
+        Array[File] arriba_pdf=glob("./output/*.pdf")
     }
 
 }