添加 'workflow.wdl'

workflow.wdl

@@ -0,0 +1,58 @@
+import "./tasks/BQSR.wdl" as Sentieon_BQSR
+
+workflow {{ }} {
+	File? deduped_bam
+    File? deduped_bam_bai
+    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 Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
+			input:
+				ref_dir=ref_fasta_dir,
+				dbsnp_dir=dbsnp_dir,
+				dbmills_dir = dbmills_dir,
+				sample_id=sample_id+'_N',
+				ref_fasta=ref_fasta,
+				dbsnp=dbsnp,
+				db_mills=db_mills,
+				deduped_bam=deduped_bam,
+				deduped_bam_index=deduped_bam_bai,
+				regions=regions,
+				interval_padding=interval_padding,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size,
+				SENTIEON_LICENSE=SENTIEON_LICENSE
+		}
+
+
+
+}