Update: README.md

README.md

 ### New Releases
 * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
 * The `corealigner` step has been removed.
+* The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`.
 
 ### Getting Started
 

tasks/TNseq.wdl

-task TNseq {
-	File ref_dir
-	File dbsnp_dir
-	File? regions
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String tumor_name
-	String normal_name
-	String docker
-	String cluster_config
-
-	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
-	String dbsnp
-	String disk_size
-
-	Boolean set_pon
-	String? cosmic_vcf
-	File? cosmic_dir
-	File? pon_vcf
-	
-	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-
-		if ${set_pon}; then
-			mkdir -p /cromwell_root/tmp/PON/
-			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
-			cp ${pon_vcf} /cromwell_root/tmp/PON/
-			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
-			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
-		fi
-		
-		if [ ${regions} != "" ]; then
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
-		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
-		fi
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
-		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
-	}
-}

tasks/corealigner.wdl

-task corealigner {
-	
-	File ref_dir
-	File dbsnp_dir
-	File dbmills_dir
-
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String docker
-	String cluster_config
-	String fasta
-
-	String dbsnp
-	String db_mills
-	File tumor_recaled_bam
-	File tumor_recaled_bam_index
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	String disk_size
-
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${tumor_recaled_bam} -i ${normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sample}_corealigned.bam				
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File corealigner_bam = "${sample}_corealigned.bam"
-		File corealigner_bam_index = "${sample}_corealigned.bam.bai"
-	}	
-}
-
-
-

workflow.wdl

         }
     }
     
-    call corealigner.corealigner as corealigner {
-        input:
-        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-        SENTIEON_LICENSE=SENTIEON_LICENSE,
-        fasta=fasta,
-        ref_dir=ref_dir,
-        sample=sample_id,
-        docker=sentieon_docker,
-        db_mills=db_mills,
-        dbmills_dir=dbmills_dir,
-        dbsnp=dbsnp,
-        dbsnp_dir=dbsnp_dir,
-        tumor_recaled_bam=tumor_BQSR.recaled_bam,
-        tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
-        normal_recaled_bam=normal_BQSR.recaled_bam,
-        normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-        disk_size=disk_size,
-        cluster_config=cluster_config
-    }
-    
     if (tnseq) {
         call TNseq.TNseq as TNseq {
             input:
             fasta=fasta,
             ref_dir=ref_dir,
             regions=regions,
-            corealigner_bam=corealigner.corealigner_bam,
-            corealigner_bam_index=corealigner.corealigner_bam_index,
+            normal_recaled_bam=normal_BQSR.recaled_bam,
+            normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+            normal_recal_table=normal_BQSR.recal_table,
+            tumor_recaled_bam=tumor_BQSR.recaled_bam,
+            tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+            tumor_recal_table=tumor_BQSR.recal_table,
             dbsnp=dbsnp,
             dbsnp_dir=dbsnp_dir,
             set_pon=set_pon,
             fasta=fasta,
             ref_dir=ref_dir,
             regions=regions,
-            corealigner_bam=corealigner.corealigner_bam,
-            corealigner_bam_index=corealigner.corealigner_bam_index,
+            normal_recaled_bam=normal_BQSR.recaled_bam,
+            normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+            normal_recal_table=normal_BQSR.recal_table,
+            tumor_recaled_bam=tumor_BQSR.recaled_bam,
+            tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+            tumor_recal_table=tumor_BQSR.recal_table,
             dbsnp=dbsnp,
             dbsnp_dir=dbsnp_dir,
             set_pon=set_pon,