revise fastqscreen

tasks/ballgown.wdl

 task ballgown {
     File gene_abundance
-    String base = basename(gene_abundance, ".gene.abundance.txt")
+    String base=basename(gene_abundance, ".gene.abundance.txt")
     Array[File] ballgown
     String docker
     String cluster
     }
     
     output {
-      File mat_expression = "${base}.txt"
+      File mat_expression="${base}.txt"
     }
 }

tasks/fastqc.wdl

 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
-		File read1_zip = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
-		File read2_html = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
-		File read2_zip = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+		File read1_html=sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File read1_zip=sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+		File read2_html=sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File read2_zip=sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
 	}
 }

tasks/fastqscreen.wdl

 		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}
+		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 ${read2}
 	>>>
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File png1 = "${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 = "${read2name}_screen.html"
+		File png1="${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/hisat2.wdl

    }
 
    output {
-      File sam = base + ".sam"
-      File unmapread_1p = base + "_un.fq.1.gz"
-      File unmapread_2p = base + "_un.fq.2.gz"
+      File sam=base + ".sam"
+      File unmapread_1p=base + "_un.fq.1.gz"
+      File unmapread_2p=base + "_un.fq.2.gz"
    }
 }

workflow.wdl

 		input:
 		read1=read1,
 		read2=read2,
-		docker = fastqc_docker,
-		cluster = fastqc_cluster,
-		disk_size = disk_size
+		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
+		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 hisat2.hisat2 as hisat2 {
 		input: 
-		docker = hisat2_docker,
-		cluster = hisat2_cluster,
+		docker=hisat2_docker,
+		cluster=hisat2_cluster,
 		idx=idx, 
 		idx_prefix=idx_prefix, 
 		read_1P=read1, 
 		read_2P=read2,
-		disk_size= disk_size
+		disk_size=disk_size
 		}
 
 	call samtools.samtools as samtools {
 		input: 
-		docker = samtools_docker,
-		cluster = samtools_cluster,
-		sam = hisat2.sam,
-		disk_size= disk_size
+		docker=samtools_docker,
+		cluster=samtools_cluster,
+		sam=hisat2.sam,
+		disk_size=disk_size
 		}
 
 	call qualimap.qualimap as qualimap {
 		input:
-		bam = samtools.out_bam,
-		bai = samtools.out_bam_index,
-		gtf = gtf, 
-		docker = qualimap_docker,
-		cluster = qualimap_cluster,
-		disk_size = disk_size
+		bam=samtools.out_bam,
+		bai=samtools.out_bam_index,
+		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_bam,
-		disk_size = disk_size
+		docker=stringtie_docker,
+		cluster=stringtie_cluster,
+		gtf=gtf, 
+		bam=samtools.out_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
+		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
+		sample_id=sample_id,
+		docker=count_docker,
+		cluster=count_cluster,
+		ballgown=stringtie.ballgown,
+		disk_size=disk_size,
+		count_length=count_length
 	}
 }