上传文件至 'tasks'

tasks/samtools.wdl

@@ -13,6 +13,7 @@ task samtools {
        /opt/conda/bin/samtools view -bS ${sam} > ${bam}
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
+       /opt/conda/bin/samtools stats -i 8000 ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size
     >>>
 
     runtime {
@@ -25,6 +26,7 @@ task samtools {
     output {
       File out_bam = sorted_bam
       File out_bam_index = sorted_bam_index
+      File out_ins_size = ins_size
     }
 
 }

tasks/stringtie.wdl

@@ -8,7 +8,7 @@ task stringtie {
     command <<<
       nt=$(nproc)
       mkdir ballgown
-      /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${base}/${base}.gtf -C ${base}.cov.ref.gtf -A ${base}.gene.abundance.txt ${bam}
+      /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${base}/${base}.gtf -C ${base}.cov.ref.gtf -A ${base}.gene.abundance.txt ${bam} -g ${sample_id}_genecount.csv
     >>>
     
     runtime {