revise workflow

workflow.wdl

 	Int qualified_quality_phred
 	Int length_required1
 	Int disable_quality_filtering
-    Int insert_size
+	Int insert_size
 
 	Boolean pre_alignment_qc
 	Boolean qualimap_qc
 	if (pre_alignment_qc) {
 		
 		call fastqc.fastqc as fastqc {
-		input:
-		read1=read1,
-		read2=read2,
-		docker=fastqc_docker,
-		cluster=fastqc_cluster,
-		disk_size=disk_size
-		}
+			input:
+			read1=read1,
+			read2=read2,
+			docker=fastqc_docker,
+			cluster=fastqc_cluster,
+			disk_size=disk_size
+			}
 		
 		call fastqscreen.fastqscreen as fastqscreen {
-		input:
-		read1=read1,
-		read2=read2,
-		docker=fastqscreen_docker,
-		cluster=fastqscreen_cluster,
-		screen_ref_dir=screen_ref_dir,
-		fastq_screen_conf=fastq_screen_conf,
-		disk_size=disk_size
-		}	
-	}
+			input:
+			read1=read1,
+			read2=read2,
+			docker=fastqscreen_docker,
+			cluster=fastqscreen_cluster,
+			screen_ref_dir=screen_ref_dir,
+			fastq_screen_conf=fastq_screen_conf,
+			disk_size=disk_size
+			}	
+			}
 	
 	if (fastp_run){
 
 		call fastp.fastp as fastp {
-		input: 
-		sample_id=sample_id, 
-		read1=read1, 
-		read2=read2,
-		docker=fastp_docker,
-		cluster=fastp_cluster,
-		disk_size=disk_size,
-		adapter_sequence=adapter_sequence,
-		adapter_sequence_r2=adapter_sequence_r2,
-		umi_loc=umi_loc,
-		trim_front1=trim_front1,
-		trim_tail1=trim_tail1, 
-		max_len1=max_len1,
-		trim_front2=trim_front2,
-		trim_tail2=trim_tail2,
-		max_len2=max_len2,
-		disable_adapter_trimming=disable_adapter_trimming,
-		length_required=length_required,
-		umi_len=umi_len,
-		UMI=UMI,
-		qualified_quality_phred=qualified_quality_phred,
-		length_required1=length_required1,
-		disable_quality_filtering=disable_quality_filtering
-		}
+			input: 
+			sample_id=sample_id, 
+			read1=read1, 
+			read2=read2,
+			docker=fastp_docker,
+			cluster=fastp_cluster,
+			disk_size=disk_size,
+			adapter_sequence=adapter_sequence,
+			adapter_sequence_r2=adapter_sequence_r2,
+			umi_loc=umi_loc,
+			trim_front1=trim_front1,
+			trim_tail1=trim_tail1, 
+			max_len1=max_len1,
+			trim_front2=trim_front2,
+			trim_tail2=trim_tail2,
+			max_len2=max_len2,
+			disable_adapter_trimming=disable_adapter_trimming,
+			length_required=length_required,
+			umi_len=umi_len,
+			UMI=UMI,
+			qualified_quality_phred=qualified_quality_phred,
+			length_required1=length_required1,
+			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, 
-		read_2P=fastp.Trim_R2,
-		docker=hisat2_docker,
-		cluster=hisat2_cluster,
-		disk_size=disk_size
-	}
-	}
+			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,
+			disk_size=disk_size
+			}
+			}
 
 	if (!fastp_run){
 		call hisat2.hisat2 as hisat2 {
-		input: 
-		docker=hisat2_docker,
-		cluster=hisat2_cluster,
-		idx=idx, 
-		idx_prefix=idx_prefix, 
-		read_1P=read1, 
-		read_2P=read2,
-		disk_size=disk_size
-		}
-	}
+			input: 
+			docker=hisat2_docker,
+			cluster=hisat2_cluster,
+			idx=idx, 
+			idx_prefix=idx_prefix, 
+			read_1P=read1, 
+			read_2P=read2,
+			disk_size=disk_size
+			}
+			}
 	
 	call samtools.samtools as samtools {
 		input: 
 
 	if (qualimap_qc){
 		call qualimap.qualimap as qualimap {
-		input:
-		bam=samtools.out_sort_bam,
-		gtf=gtf, 
-		docker=qualimap_docker,
-		cluster=qualimap_cluster,
-		disk_size=disk_size
-		}
-	}
+			input:
+			bam=samtools.out_sort_bam,
+			gtf=gtf, 
+			docker=qualimap_docker,
+			cluster=qualimap_cluster,
+			disk_size=disk_size
+			}
+			}
 
 	call stringtie.stringtie as stringtie {
 		input: