更新 'tasks/arriba.wdl'

gz

tasks/arriba.wdl

@@ -16,38 +16,16 @@ task arriba{
         set -e
         gzip -c ${fastq1} >${sample_id}_R1.fastq.gz
         gzip -c ${fastq2} >${sample_id}_R2.fastq.gz
-        mkdir ./output/
-        STAR \
-            --runThreadN 4 \
-            --genomeDir ${STAR_INDEX_DIR} \
-            --genomeLoad NoSharedMemory \
-            --readFilesIn ${sample_id}_R1.fastq.gz ${sample_id}_R2.fastq.gz \
-            --readFilesCommand zcat \
-            --outStd BAM_Unsorted \
-            --outSAMtype BAM Unsorted \
-            --outSAMunmapped Within \
-            --outBAMcompression 0 \
-            --outFilterMultimapNmax 50 \
-            --peOverlapNbasesMin 10 \
-            --alignSplicedMateMapLminOverLmate 0.5 \
-            --alignSJstitchMismatchNmax 5 -1 5 5 \
-            --chimSegmentMin 10 \
-            --chimOutType WithinBAM HardClip \
-            --chimJunctionOverhangMin 10 \
-            --chimScoreDropMax 30 \
-            --chimScoreJunctionNonGTAG 0 \
-            --chimScoreSeparation 1 \
-            --chimSegmentReadGapMax 3 \
-            --chimMultimapNmax 50 |tee ./output/${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} \
-            -b /arriba_v2.1.0/database/blacklist_hg38_GRCh38_v2.1.0.tsv.gz \
-            -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
+        
+        mkdir ./output/      
+        echo ${star_index_dir} >output/a.txt
+        echo ${fastq1} >> output/a.txt
+        echo ${fastq2} >> output/a.txt
+        echo ${sample_id} >> output/a.txt
+        echo ${assembly_fa} >> output/a.txt
+        echo ${annotation_gtf} >> output/a.txt
 
+       
 
     >>>
 	
@@ -59,9 +37,8 @@ task arriba{
     }
 
     output {
-        Array[File] arriba_result=glob("./output/*.tsv")
+        Array[File] arriba_result=glob("./output/*.txt")
         Array[File] arriba_gz=glob("./output/*.gz")
-        Array[File] arriba_bam=glob("./output/*.bam")
     }
 
 }