上传文件至 'tasks'

tasks/hisat2.wdl

 task hisat2 {
    File idx
-   File read_1P
-   File read_2P
+   File read1
+   File read2
    String idx_prefix
-   String base = sub(basename(read_1P),"\\.\\S+$", "")
+   String sample_id
    String docker
    String cluster
 
    command {
    	 nt=$(nproc)
-     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam  --un-conc-gz ${base}_un.fq.gz
+     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read1} -2 ${read2} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
    }
    
    runtime { 
    }
 
    output {
-      File sam = base + ".sam"
-      File unmapread_1p = base + "_un.fq.1.gz"
-      File unmapread_2p = base + "_un.fq.2.gz"
+      File sam = "${sample_id}.sam"
+      File unmapread_1p = "${sample_id}_un.fq.1.gz"
+      File unmapread_2p = "${sample_id}_un.fq.2.gz"
    }
 }

tasks/samtools.wdl

 task samtools {
     File sam
-    String base = basename(sam, ".sam")
-    String bam = base + ".bam"
-    String sorted_bam = base + ".sorted.bam"
-    String sorted_bam_index = base + ".sorted.bam.bai"
+    String sample_id
+    String bam = sample_id + ".bam"
+    String sorted_bam = sample_id + ".sorted.bam"
+    String sorted_bam_index = sample_id + ".sorted.bam.bai"
+    String ins_size = sample_id + ".ins_size"
     String docker
     String cluster
 

tasks/stringtie.wdl

     File bam
     File gtf
     String docker
-    String base = basename(bam, ".sorted.bam")
+    String sample_id
     String cluster
 
     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} -g ${sample_id}_genecount.csv
+      /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 {
     }
     
     output {
-      File covered_transcripts = "${base}.cov.ref.gtf"
-      File gene_abundance = "${base}.gene.abundance.txt"
-      Array[File] ballgown = ["ballgown/${base}/${base}.gtf", "ballgown/${base}/e2t.ctab", "ballgown/${base}/e_data.ctab", "ballgown/${base}/i2t.ctab", "ballgown/${base}/i_data.ctab", "ballgown/${base}/t_data.ctab"]
+      File covered_transcripts = "${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"
     }
 }