......

workflow.wdl

@@ -65,126 +65,7 @@ workflow {{ project_name }} {
 	Int qualimapRNAseq_disk_size
 	Int insert_size
 	Int minimum_length_allowed_for_the_predicted_transcripts
-    Int Junctions_no_spliced_reads
-    Float minimum_isoform_abundance
-    Float maximum_fraction_of_muliplelocationmapped_reads
-
-	scatter (quartet in inputSamples){
-
-		call fastp.fastp as fastp {
-		input: 
-		sample_id= quartet[2],
-		read1= quartet[0], 
-		read2= quartet[1],
-		docker = fastp_docker,
-		cluster = fastp_cluster,
-		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 fastqc.fastqc as fastqc {
-		input:
-		read1=fastp.Trim_R1, 
-		read2=fastp.Trim_R2,
-		docker=fastqc_docker,
-		cluster_config=fastqc_cluster_config,
-		disk_size=fastqc_cluster_config
-		}
-
-		call fastqscreen.fastq_screen as fastqscreen {
-		input:
-		read1=fastp.Trim_R1, 
-		read2=fastp.Trim_R2,
-		screen_ref_dir=screen_ref_dir,
-		fastq_screen_conf=fastq_screen_conf,
-		docker = fastqscreen_docker,
-		cluster_config = fastqscreen_cluster_config,
-		disk_size= fastqscreen_disk_size
-		}
-
-		call hisat2.hisat2 as hisat2 {
-		input: 
-		sample_id = quartet[2],
-		idx = idx, 
-		idx_prefix = idx_prefix, 
-		Trim_R1 = fastp.Trim_R1, 
-		Trim_R2 = fastp.Trim_R2,
-		docker = hisat2_docker,
-		cluster = hisat2_cluster,
-		pen_intronlen = pen_intronlen,
-		pen_cansplice = pen_cansplice,
-		pen_noncansplice = pen_noncansplice,
-		min_intronlen = min_intronlen,
-		max_intronlen = max_intronlen,
-		maxins = maxins,
-		minins = minins
-		}
-
-		call samtools.samtools as samtools {
-		input: 
-		sample_id = quartet[2],
-		sam = hisat2.sam,
-        docker = samtools_docker,
-		cluster = samtools_cluster,
-		insert_size = insert_size
-		}
-        
-        call qualimapBAMqc.qualimapBAMqc as qualimapBAMqc {
-		input:
-		bam = samtools.out_percent,
-		docker = qualimapBAMqc_docker,
-		cluster_config = qualimapBAMqc_cluster_config,
-		disk_size = qualimapBAMqc_disk_size
-		}
-
-		call qualimapRNAseq.qualimapRNAseq as qualimapRNAseq {
-		input:
-		bam = samtools.out_percent,
-		docker = qualimapRNAseq_docker,
-		cluster_config = qualimapRNAseq_cluster_config,
-		disk_size = qualimapRNAseq_disk_size,
-		gtf = gtf
-		}
-
-		call stringtie.stringtie as stringtie {
-		input: 
-		sample_id = quartet[2],
-		gtf = gtf, 
-		bam = samtools.out_bam,
-		docker = stringtie_docker,
-		cluster = stringtie_cluster,
-		minimum_length_allowed_for_the_predicted_transcripts = minimum_length_allowed_for_the_predicted_transcripts,
-    	Junctions_no_spliced_reads = Junctions_no_spliced_reads,
-    	minimum_isoform_abundance = minimum_isoform_abundance,
-    	maximum_fraction_of_muliplelocationmapped_reads = maximum_fraction_of_muliplelocationmapped_reads
-		}
-	}
-
-
-	call multiqc.multiqc as multiqc {
-	input:
-	docker = multiqc_docker,
-	cluster_config = multiqc_cluster_config,
-	disk_size = multiqc_disk_size,
-	read1_zip = fastqc.read1_zip,
-	read2_zip = fastqc.read2_zip,
-	txt1 = fastqscreen.txt1,
-	txt2 = fastqscreen.txt2,
-	bamqc_zip = qualimapBAMqc.bamqc_zip,
-	RNAseqqc_zip = qualimapRNAseq.rnaseq_zip
-	}
+    	Int Junctions_no_spliced_reads
+   	Float minimum_isoform_abundance
+    	Float maximum_fraction_of_muliplelocationmapped_reads
 }