revise workflow

defaults

 {
-    "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/", 
+    "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
     "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
     "idx_prefix": "genome_snp_tran",
     "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

tasks/hisat2.wdl

    }
    
    runtime { 
-      docker: docker 
+      docker: docker
       cluster: cluster
       systemDisk: "cloud_ssd 40"
       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

tasks/hisat2_fp.wdl

+task hisat2_fp {
+   File idx
+   File read_1P
+   File read_2P
+   String idx_prefix
+   String sample_id
+   String docker
+   String cluster
+   String disk_size
+   
+
+   command {
+      nt=$(nproc)
+      hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
+   }
+   
+   runtime { 
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd " + disk_size + " /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"
+   }
+}

tasks/samtools.wdl

     String sorted_bam=base + ".sorted.bam"
     String sorted_bam_index=base + ".sorted.bam.bai"
     String samstats=base + ".samstats"
-    String ins_size=base + ".ins_size" 
+    String ins_size=base + ".ins_size"
     String docker
     String cluster
     String disk_size

workflow.wdl

 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/fastp.wdl" as fastp
 import "./tasks/qualimap.wdl" as qualimap
+import "./tasks/hisat2_fp.wdl" as hisat2_fp
 import "./tasks/hisat2.wdl" as hisat2
 import "./tasks/samtools.wdl" as samtools
 import "./tasks/stringtie.wdl" as stringtie
 	String count_length
 	String sample_id
 
-	Int trim_front1 
-	Int trim_tail1 
-	Int max_len1 
-	Int trim_front2 
-	Int trim_tail2  
-	Int max_len2 
+	Int trim_front1
+	Int trim_tail1
+	Int max_len1
+	Int trim_front2
+	Int trim_tail2
+	Int max_len2
 	Int disable_adapter_trimming
 	Int length_required
 	Int umi_len
 	Boolean fastp_run
 	
 	if (pre_alignment_qc) {
-		
 		call fastqc.fastqc as fastqc {
 			input:
 			read1=read1,
 			}
 	
 	if (fastp_run){
-
 		call fastp.fastp as fastp {
-			input: 
-			sample_id=sample_id, 
-			read1=read1, 
+			input:
+			sample_id=sample_id,
+			read1=read1,
 			read2=read2,
 			docker=fastp_docker,
 			cluster=fastp_cluster,
 			adapter_sequence_r2=adapter_sequence_r2,
 			umi_loc=umi_loc,
 			trim_front1=trim_front1,
-			trim_tail1=trim_tail1, 
+			trim_tail1=trim_tail1,
 			max_len1=max_len1,
 			trim_front2=trim_front2,
 			trim_tail2=trim_tail2,
 			disable_quality_filtering=disable_quality_filtering
 			}
 
-		call hisat2.hisat2 as hisat2 {
-			input: 
-			sample_id=sample_id, 
-			idx=idx, 
-			idx_prefix=idx_prefix, 
-			read_1P=fastp.Trim_R1, 
+		call hisat2.hisat2_fp as hisat2_fp {
+			input:
+			sample_id=sample_id,
+			idx=idx,
+			idx_prefix=idx_prefix,
+			read_1P=fastp.Trim_R1,
 			read_2P=fastp.Trim_R2,
 			docker=hisat2_docker,
 			cluster=hisat2_cluster,
 
 	if (!fastp_run){
 		call hisat2.hisat2 as hisat2 {
-			input: 
+			input:
+			sample_id=sample_id,
 			docker=hisat2_docker,
 			cluster=hisat2_cluster,
-			idx=idx, 
-			idx_prefix=idx_prefix, 
-			read_1P=read1, 
+			idx=idx,
+			idx_prefix=idx_prefix,
+			read_1P=read1,
 			read_2P=read2,
 			disk_size=disk_size
 			}
 			}
 	
 	call samtools.samtools as samtools {
-		input: 
+		input:
 		docker=samtools_docker,
 		cluster=samtools_cluster,
 		sam=hisat2.sam,
-		insert_size = insert_size,
+		insert_size=insert_size,
 		disk_size=disk_size
 		}
 
 		call qualimap.qualimap as qualimap {
 			input:
 			bam=samtools.out_sort_bam,
-			gtf=gtf, 
+			gtf=gtf,
 			docker=qualimap_docker,
 			cluster=qualimap_cluster,
 			disk_size=disk_size
 			}
 
 	call stringtie.stringtie as stringtie {
-		input: 
+		input:
 		docker=stringtie_docker,
 		cluster=stringtie_cluster,
-		gtf=gtf, 
+		gtf=gtf,
 		bam=samtools.out_sort_bam,
 		disk_size=disk_size
 		}
 
 	call ballgown.ballgown as ballgown {
-		input: 
+		input:
 		docker=ballgown_docker,
 		cluster=ballgown_cluster,
 		ballgown=stringtie.ballgown,
 		gene_abundance=stringtie.gene_abundance,
 		disk_size=disk_size
-		} 
+		}
 	
 	call count.count as count {
-		input: 
+		input:
 		sample_id=sample_id,
 		docker=count_docker,
 		cluster=count_cluster,