添加 'workflow_bamQC.wdl'

workflow_bamQC.wdl

@@ -0,0 +1,109 @@
+#Only for BamQC
+import "./tasks/fastqTobam.wdl" as fastqTobam
+import "./tasks/qualimap.wdl" as qualimap
+import "./tasks/BQSR.wdl" as Sentieon_BQSR
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNscope.wdl" as TNscope
+import "./tasks/manta.wdl" as manta_calling
+import "./tasks/strelka.wdl" as strelka_calling
+
+
+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 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
+
+
+if (normal_in1 != ""){
+	
+		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_normal{
+			input:
+				fastq1=normal_in1,
+				fastq2=normal_in2,
+				sample_id=sample_id+'_N',
+				Seq_platform=Seq_platform,
+				ref_fasta=ref_fasta,
+				ref_fasta_dir=ref_fasta_dir,
+				SENTIEON_LICENSE=SENTIEON_LICENSE,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size
+
+		}
+
+		call qualimap.qualimap as qualimap_normal{
+				 input:
+				 sample_id=sample_id+'_N',
+				 bam_file=SentieonFastqToBam_normal.deduped_bam,
+				 bam_bai=SentieonFastqToBam_normal.deduped_bam_bai,
+				 annot_gff=annot_gff,
+				 docker=docker_qualimap,
+				 cluster_config=cluster_config,
+				 disk_size=disk_size
+			}
+
+
+	}
+
+if (tumor_in1 != ""){
+
+		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_tumor{
+			input:
+				fastq1=tumor_in1,
+				fastq2=tumor_in2,
+				sample_id=sample_id+'_T',
+				Seq_platform=Seq_platform,
+				ref_fasta=ref_fasta,
+				ref_fasta_dir=ref_fasta_dir,
+				SENTIEON_LICENSE=SENTIEON_LICENSE,
+				docker=docker_sentieon,
+				cluster_config=cluster_config,
+				disk_size=disk_size
+
+		}
+
+		call qualimap.qualimap as qualimap_tumor{
+				 input:
+				 sample_id=sample_id+'_T',
+				 bam_file=SentieonFastqToBam_tumor.deduped_bam,
+				 bam_bai=SentieonFastqToBam_tumor.deduped_bam_bai,
+				 annot_gff=annot_gff,
+				 docker=docker_qualimap,
+				 cluster_config=cluster_config,
+				 disk_size=disk_size
+			}
+
+
+
+	}
+
+
+}