Improve indentation.

tasks/fastqc.wdl

 task fastqc {
-	File read1
-	File read2
-	String docker
-	String read1name=sub(basename(read1),"\\.\\S+$", "")
-	String read2name=sub(basename(read2),"\\.\\S+$", "")
-	String cluster
-	String disk_size
+  File read1
+  File read2
+  String docker
+  String read1name=sub(basename(read1),"\\.\\S+$", "")
+  String read2name=sub(basename(read2),"\\.\\S+$", "")
+  String cluster
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		fastqc -t $nt -o ./ ${read1}
-		fastqc -t $nt -o ./ ${read2}
-	>>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    fastqc -t $nt -o ./ ${read1}
+    fastqc -t $nt -o ./ ${read2}
+  >>>
 
-	runtime {
-		docker:docker
-		cluster: cluster
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File read1_html="${read1name}_fastqc.html"
-		File read1_zip="${read1name}_fastqc.zip"
-		File read2_html="${read2name}_fastqc.html"
-		File read2_zip="${read1name}_fastqc.zip"
-	}
+  runtime {
+    docker:docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File read1_html="${read1name}_fastqc.html"
+    File read1_zip="${read1name}_fastqc.zip"
+    File read2_html="${read2name}_fastqc.html"
+    File read2_zip="${read1name}_fastqc.zip"
+  }
 }

tasks/fastqscreen.wdl

 task fastqscreen {
-	File read1
-	File read2
-	File screen_ref_dir
-	File fastq_screen_conf
-	String read1name=sub(basename(read1),"\\.\\S+$", "")
-	String read2name=sub(basename(read2),"\\.\\S+$", "")
-	String docker
-	String cluster
-	String disk_size
+  File read1
+  File read2
+  File screen_ref_dir
+  File fastq_screen_conf
+  String read1name=sub(basename(read1),"\\.\\S+$", "")
+  String read2name=sub(basename(read2),"\\.\\S+$", "")
+  String docker
+  String cluster
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp
-		cp -r ${screen_ref_dir} /cromwell_root/tmp/
-		# sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
-	>>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp
+    cp -r ${screen_ref_dir} /cromwell_root/tmp/
+    # sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
+  >>>
 
-	runtime {
-		docker:docker
-		cluster: cluster
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File png1="${read1name}_screen.png"
-		File txt1="${read1name}_screen.txt"
-		File html1="${read1name}_screen.html"
-		File png2="${read2name}_screen.png"
-		File txt2="${read2name}_screen.txt"
-		File html2="${read2name}_screen.html"
-	}
+  runtime {
+    docker:docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File png1="${read1name}_screen.png"
+    File txt1="${read1name}_screen.txt"
+    File html1="${read1name}_screen.html"
+    File png2="${read2name}_screen.png"
+    File txt2="${read2name}_screen.txt"
+    File html2="${read2name}_screen.html"
+  }
 }

tasks/qualimap.wdl

 task qualimap {
-	File bam
-	File gtf
-	String bamname=basename(bam, ".sorted.bam")
-	String docker
-	String cluster
-	String disk_size
+  File bam
+  File gtf
+  String bamname=basename(bam, ".sorted.bam")
+  String docker
+  String cluster
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
-		tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
-	>>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+    tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
+  >>>
 
-	runtime {
-		docker: docker
-		cluster: cluster
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-	output {
-		File bamqc_gz="${bamname}_bamqc_qualimap.tar.gz"
-	}
+  output {
+    File bamqc_gz="${bamname}_bamqc_qualimap.tar.gz"
+  }
 }

workflow.wdl

 import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
-	File read1
-	File read2
-	File idx
-	File screen_ref_dir
-	File fastq_screen_conf
-	File gtf
+  File read1
+  File read2
+  File idx
+  File screen_ref_dir
+  File fastq_screen_conf
+  File gtf
 
-	String disk_size
-	String fastqc_docker
-	String fastqc_cluster
-	String fastqscreen_docker
-	String fastqscreen_cluster
-	String fastp_docker
-	String fastp_cluster
-	String adapter_sequence
-	String adapter_sequence_r2
-	String hisat2_docker
-	String hisat2_cluster
-	String idx_prefix
-	String stringtie_docker
-	String stringtie_cluster
-	String samtools_docker
-	String samtools_cluster
-	String qualimap_docker
-	String qualimap_cluster
-	String ballgown_docker
-	String ballgown_cluster
-	String count_docker
-	String count_cluster
-	String count_length
-	String sample_id
+  String disk_size
+  String fastqc_docker
+  String fastqc_cluster
+  String fastqscreen_docker
+  String fastqscreen_cluster
+  String fastp_docker
+  String fastp_cluster
+  String adapter_sequence
+  String adapter_sequence_r2
+  String hisat2_docker
+  String hisat2_cluster
+  String idx_prefix
+  String stringtie_docker
+  String stringtie_cluster
+  String samtools_docker
+  String samtools_cluster
+  String qualimap_docker
+  String qualimap_cluster
+  String ballgown_docker
+  String ballgown_cluster
+  String count_docker
+  String count_cluster
+  String count_length
+  String sample_id
 
-	Int insert_size
+  Int insert_size
 
-	Boolean pre_alignment_qc
-	Boolean qualimap_qc
-	Boolean trim_adapter
-	
-	if (pre_alignment_qc) {
-		call fastqc.fastqc as fastqc {
-			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
-		}	
-	}
+  Boolean pre_alignment_qc
+  Boolean qualimap_qc
+  Boolean trim_adapter
+  
+  if (pre_alignment_qc) {
+    call fastqc.fastqc as fastqc {
+      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
+    }	
+  }
 
-	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,
-		trim_adapter=trim_adapter
-	}
-			
-	call hisat2.hisat2 as hisat2 {
-		input:
-		sample_id=sample_id,
-		docker=hisat2_docker,
-		cluster=hisat2_cluster,
-		idx=idx,
-		idx_prefix=idx_prefix,
-		read_1P=fastp.trim_R1,
-		read_2P=fastp.trim_R2,
-		disk_size=disk_size
-	}
-	
-	call samtools.samtools as samtools {
-		input:
-		docker=samtools_docker,
-		cluster=samtools_cluster,
-		sam=hisat2.sam,
-		insert_size=insert_size,
-		disk_size=disk_size
-	}
+  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,
+    trim_adapter=trim_adapter
+  }
+      
+  call hisat2.hisat2 as hisat2 {
+    input:
+    sample_id=sample_id,
+    docker=hisat2_docker,
+    cluster=hisat2_cluster,
+    idx=idx,
+    idx_prefix=idx_prefix,
+    read_1P=fastp.trim_R1,
+    read_2P=fastp.trim_R2,
+    disk_size=disk_size
+  }
+  
+  call samtools.samtools as samtools {
+    input:
+    docker=samtools_docker,
+    cluster=samtools_cluster,
+    sam=hisat2.sam,
+    insert_size=insert_size,
+    disk_size=disk_size
+  }
 
-	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
-		}
-	}
+  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
+    }
+  }
 
-	call stringtie.stringtie as stringtie {
-		input:
-		docker=stringtie_docker,
-		cluster=stringtie_cluster,
-		gtf=gtf,
-		bam=samtools.out_sort_bam,
-		disk_size=disk_size
-	}
+  call stringtie.stringtie as stringtie {
+    input:
+    docker=stringtie_docker,
+    cluster=stringtie_cluster,
+    gtf=gtf,
+    bam=samtools.out_sort_bam,
+    disk_size=disk_size
+  }
 
-	call ballgown.ballgown as ballgown {
-		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:
-		sample_id=sample_id,
-		docker=count_docker,
-		cluster=count_cluster,
-		ballgown=stringtie.ballgown,
-		disk_size=disk_size,
-		count_length=count_length
-	}
+  call ballgown.ballgown as ballgown {
+    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:
+    sample_id=sample_id,
+    docker=count_docker,
+    cluster=count_cluster,
+    ballgown=stringtie.ballgown,
+    disk_size=disk_size,
+    count_length=count_length
+  }
 }