添加 'workflow.wdl'

workflow.wdl

@@ -0,0 +1,63 @@
+import "./tasks/TNseq.wdl" as TNseq
+
+workflow {{ project_name }} {
+	#sample info
+    File? normal_in1
+    File? normal_in2
+	File? tumor_in1
+	File? tumor_in2
+    String sample_id
+	String Seq_platform
+	#reference fasta
+	String ref_fasta
+	File ref_fasta_dir
+	File annot_gff
+    File dbsnp_dir
+    File dbmills_dir
+    String dbsnp
+    String db_mills
+    File? regions
+    Int? interval_padding
+	File germline_resource
+	File germline_resource_tbi
+
+	#docker
+    String docker_fastp
+	String docker_sentieon
+	String SENTIEON_LICENSE
+	String docker_qualimap
+	String docker_manta
+	String docker_strelka
+
+	#config
+    String cluster_config
+    String disk_size
+	Boolean? fastqc
+	Boolean bamqc
+
+
+	call TNseq.sentieon_TNseq as sentieon_TNseq{
+	input:
+		sample_id = sample_id,
+		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
+		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
+		normal_bam = Sentieon_BQSR_normal.recaled_bam,
+		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		tumor_name = sample_id+'_T',
+		normal_name = sample_id+'_N',
+
+		ref_dir = ref_fasta_dir,
+		ref_fasta = ref_fasta,
+		germline_resource = germline_resource,
+		germline_resource_tbi = germline_resource_tbi,
+
+		docker = docker_sentieon,
+		cluster_config = cluster_config,
+		disk_size = disk_size,
+		SENTIEON_LICENSE = SENTIEON_LICENSE
+}
+
+}
+
+
+