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hisat2.wdl

+task hisat2 {
+   File idx
+   File read1
+   File read2
+   String idx_prefix
+   String sample_id
+   String docker
+   String cluster
+
+   command {
+   	 nt=$(nproc)
+     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read1} -2 ${read2} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
+   }
+   
+   runtime { 
+		docker: docker 
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd 200 /cromwell_root/"
+   }
+
+   output {
+      File sam = "${sample_id}.sam"
+      File unmapread_1p = "${sample_id}_un.fq.1.gz"
+      File unmapread_2p = "${sample_id}_un.fq.2.gz"
+   }
+}

inputs

 {
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
     "{{ project_name }}.read1": "{{ read1 }}",
     "{{ project_name }}.read2": "{{ read2 }}",
     "{{ project_name }}.idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",

samtools.wdl

+task samtools {
+    File sam
+    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
+
+    command <<<
+       set -o pipefail
+       set -e
+       /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 {
+       docker: docker
+       cluster: cluster
+       systemDisk: "cloud_ssd 40"
+       dataDisk: "cloud_ssd 200 /cromwell_root/"
+    }
+
+    output {
+      File out_bam = sorted_bam
+      File out_bam_index = sorted_bam_index
+      File out_ins_size = ins_size
+    }
+
+}
+

stringtie.wdl

+task stringtie {
+    File bam
+    File gtf
+    String docker
+    String sample_id
+    String cluster
+
+    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} -g ${sample_id}_genecount.csv
+    >>>
+    
+    runtime {
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd 150 /cromwell_root/"
+    }
+    
+    output {
+      File covered_transcripts = "${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"
+    }
+}