上传文件至 'tasks'

tasks/stringtie.wdl

     command <<<
       nt=$(nproc)
       mkdir ballgown
-      /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam}
+      /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${sample_id}/${sample_id}.gtf -C ${sample_id}.cov.ref.gtf -A ${sample_id}.gene.abundance.txt ${bam} -g ${sample_id}_genecount.csv
     >>>
     
     runtime {
       File covered_transcripts = "${sample_id}.cov.ref.gtf"
       File gene_abundance = "${sample_id}.gene.abundance.txt"
       Array[File] ballgown = ["ballgown/${sample_id}/${sample_id}.gtf", "ballgown/${sample_id}/e2t.ctab", "ballgown/${sample_id}/e_data.ctab", "ballgown/${sample_id}/i2t.ctab", "ballgown/${sample_id}/i_data.ctab", "ballgown/${sample_id}/t_data.ctab"]
+      File genecount = "{sample_id}_genecount.csv"
     }
 }