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variant-calling
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Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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variant-calling/workflow.wdl

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  1. import "./tasks/mapping.wdl" as mapping

  2. import "./tasks/Metrics.wdl" as Metrics

  3. import "./tasks/Dedup.wdl" as Dedup

  4. import "./tasks/deduped_Metrics.wdl" as deduped_Metrics

  5. import "./tasks/BQSR.wdl" as BQSR

  6. import "./tasks/Haplotyper.wdl" as Haplotyper

  7. import "./tasks/TNseq.wdl" as TNseq

  8. import "./tasks/TNscope.wdl" as TNscope

  9. import "./tasks/somatic.wdl" as somatic

  10. import "./tasks/processSomatic.wdl" as processSomatic

  11. import "./tasks/somaticFilter.wdl" as somaticFilter

  12. import "./tasks/replaceRG.wdl" as replaceRG

  13. import "./tasks/Pindel.wdl" as Pindel

  14. import "./tasks/ANNOVAR.wdl" as ANNOVAR

  15. import "./tasks/VEP.wdl" as VEP

  16. 

  17. 

  18. workflow {{ project_name }} {

  19.   

  20.   String sample_id

  21.   File? tumor_fastq_1

  22.   File? tumor_fastq_2

  23.   File? normal_fastq_1

  24.   File? normal_fastq_2

  25.   File? tumor_deduped_bam

  26.   File? normal_deduped_bam

  27. 

  28.   Boolean input_fastq

  29.   Boolean input_bam

  30. 

  31.   String SENTIEON_INSTALL_DIR

  32.   String SENTIEON_LICENSE

  33.   String sentieon_docker

  34.   String varscan_docker

  35.   String pindel_docker

  36.   String samtools_docker

  37.   String annovar_docker

  38.   String vep_docker

  39. 

  40.   String pl

  41.   File ref_dir

  42.   String fasta

  43.   File dbmills_dir

  44.   String db_mills

  45.   File dbsnp_dir

  46.   String dbsnp

  47.   File germline_resource

  48.   File germline_resource_tbi

  49.   String hg

  50.   File annovar_database

  51.   

  52.   File? regions

  53.   Int? interval_padding

  54.   File? tnseq_pon

  55.   File? tnscope_pon

  56. 

  57.   String vep_path

  58.   File cache

  59.   String species

  60.   String vcf2maf_path

  61. 

  62.   String disk_size

  63.   String cluster_config

  64. 

  65.   Boolean haplotyper

  66.   Boolean pindel

  67.   Boolean tnseq

  68.   Boolean tnscope

  69.   Boolean varscan

  70. 

  71.   Boolean annovar

  72.   Boolean vep

  73. 

  74.   if (input_fastq) {

  75.     if (tumor_fastq_1!= "") {

  76.       call mapping.mapping as tumor_mapping {

  77.         input: 

  78.         group=sample_id + '.T',

  79.         sample=sample_id + '.T',

  80.         fastq_1=tumor_fastq_1,

  81.         fastq_2=tumor_fastq_2,

  82.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  83.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  84.         pl=pl,

  85.         fasta=fasta,

  86.         ref_dir=ref_dir,

  87.         docker=sentieon_docker,

  88.         disk_size=disk_size,

  89.         cluster_config=cluster_config

  90.       }

  91. 

  92.       call Metrics.Metrics as tumor_Metrics {

  93.         input:

  94.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  95.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  96.         fasta=fasta,

  97.         ref_dir=ref_dir,

  98.         sorted_bam=tumor_mapping.sorted_bam,

  99.         sorted_bam_index=tumor_mapping.sorted_bam_index,

  100.         sample=sample_id + '.T',

  101.         docker=sentieon_docker,

  102.         disk_size=disk_size,

  103.         cluster_config=cluster_config

  104.       }

  105. 

  106.       call Dedup.Dedup as tumor_Dedup {

  107.         input:

  108.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  109.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  110.         sorted_bam=tumor_mapping.sorted_bam,

  111.         sorted_bam_index=tumor_mapping.sorted_bam_index,

  112.         sample=sample_id + '.T',

  113.         docker=sentieon_docker,

  114.         disk_size=disk_size,

  115.         cluster_config=cluster_config

  116.       }

  117. 

  118.       call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {

  119.         input:

  120.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  121.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  122.         fasta=fasta,

  123.         ref_dir=ref_dir,

  124.         deduped_bam=tumor_Dedup.deduped_bam,

  125.         deduped_bam_index=tumor_Dedup.deduped_bam_index,

  126.         sample=sample_id + '.T',

  127.         docker=sentieon_docker,

  128.         disk_size=disk_size,

  129.         cluster_config=cluster_config

  130.       }

  131. 

  132.       call BQSR.BQSR as tumor_BQSR {

  133.         input:

  134.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  135.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  136.         fasta=fasta,

  137.         ref_dir=ref_dir,

  138.         deduped_bam=tumor_Dedup.deduped_bam,

  139.         deduped_bam_index=tumor_Dedup.deduped_bam_index,

  140.         db_mills=db_mills,

  141.         dbmills_dir=dbmills_dir,

  142.         dbsnp=dbsnp,

  143.         dbsnp_dir=dbsnp_dir,

  144.         sample=sample_id + '.T',

  145.         docker=sentieon_docker,

  146.         disk_size=disk_size,

  147.         cluster_config=cluster_config

  148.       }

  149.     }

  150.     

  151.     if (normal_fastq_1!= "") {

  152.       call mapping.mapping as normal_mapping {

  153.         input: 

  154.         group=sample_id + '.N',

  155.         sample=sample_id + '.N',

  156.         fastq_1=normal_fastq_1,

  157.         fastq_2=normal_fastq_2,

  158.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  159.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  160.         pl=pl,

  161.         fasta=fasta,

  162.         ref_dir=ref_dir,

  163.         docker=sentieon_docker,

  164.         disk_size=disk_size,

  165.         cluster_config=cluster_config

  166.       }

  167. 

  168.       call Metrics.Metrics as normal_Metrics {

  169.         input:

  170.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  171.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  172.         fasta=fasta,

  173.         ref_dir=ref_dir,

  174.         sorted_bam=normal_mapping.sorted_bam,

  175.         sorted_bam_index=normal_mapping.sorted_bam_index,

  176.         sample=sample_id + '.N',

  177.         regions=regions,

  178.         docker=sentieon_docker,

  179.         disk_size=disk_size,

  180.         cluster_config=cluster_config

  181.       }

  182. 

  183.       call Dedup.Dedup as normal_Dedup {

  184.         input:

  185.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  186.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  187.         sorted_bam=normal_mapping.sorted_bam,

  188.         sorted_bam_index=normal_mapping.sorted_bam_index,

  189.         sample=sample_id + '.N',

  190.         docker=sentieon_docker,

  191.         disk_size=disk_size,

  192.         cluster_config=cluster_config

  193.       }

  194. 

  195.       call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {

  196.         input:

  197.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  198.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  199.         fasta=fasta,

  200.         ref_dir=ref_dir,

  201.         deduped_bam=normal_Dedup.deduped_bam,

  202.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  203.         sample=sample_id + '.N',

  204.         regions=regions,

  205.         docker=sentieon_docker,

  206.         disk_size=disk_size,

  207.         cluster_config=cluster_config

  208.       }

  209. 

  210.       call BQSR.BQSR as normal_BQSR {

  211.         input:

  212.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  213.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  214.         fasta=fasta,

  215.         ref_dir=ref_dir,

  216.         deduped_bam=normal_Dedup.deduped_bam,

  217.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  218.         db_mills=db_mills,

  219.         dbmills_dir=dbmills_dir,

  220.         dbsnp=dbsnp,

  221.         dbsnp_dir=dbsnp_dir,

  222.         sample=sample_id + '.N',

  223.         docker=sentieon_docker,

  224.         disk_size=disk_size,

  225.         cluster_config=cluster_config

  226.       }

  227.     }

  228. 

  229.     if (haplotyper) {

  230.       call Haplotyper.Haplotyper as Haplotyper {

  231.         input:

  232.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  233.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  234.         sample=sample_id + '.N',

  235.         fasta=fasta,

  236.         ref_dir=ref_dir,

  237.         recaled_bam=normal_BQSR.recaled_bam,

  238.         recaled_bam_index=normal_BQSR.recaled_bam_index,

  239.         dbsnp=dbsnp,

  240.         dbsnp_dir=dbsnp_dir,

  241.         regions=regions,

  242.         docker=sentieon_docker,

  243.         disk_size=disk_size,

  244.         cluster_config=cluster_config

  245.       }

  246.     }

  247.      

  248.     if (pindel) {

  249.       call Pindel.Pindel as Pindel {

  250.         input:	

  251.         sample_id=sample_id + '.N',

  252.         bam=normal_BQSR.recaled_bam,

  253.         bam_index=normal_BQSR.recaled_bam_index,

  254.         fasta=fasta,

  255.         ref_dir=ref_dir,

  256.         docker=pindel_docker,

  257.         disk_size=disk_size,

  258.         cluster_config=cluster_config

  259.       }

  260.     }

  261. 

  262.     if (tnseq) {

  263.       call TNseq.TNseq as TNseq {

  264.         input:

  265.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  266.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  267.         sample=sample_id,

  268.         normal_recaled_bam=normal_BQSR.recaled_bam,

  269.         normal_recaled_bam_index=normal_BQSR.recaled_bam_index,

  270.         tumor_recaled_bam=tumor_BQSR.recaled_bam,

  271.         tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,

  272.         normal_name=sample_id + ".N",

  273.         tumor_name=sample_id + ".T",

  274.         fasta=fasta,

  275.         ref_dir=ref_dir,

  276.         regions=regions,

  277.         interval_padding=interval_padding,

  278.         germline_resource=germline_resource,

  279.         germline_resource_tbi=germline_resource_tbi,

  280.         pon_vcf=tnseq_pon,

  281.         docker=sentieon_docker,

  282.         cluster_config=cluster_config,

  283.         disk_size=disk_size

  284.       }

  285. 

  286.       if (annovar) {

  287.         call ANNOVAR.ANNOVAR as TNseq_annovar {

  288.           input:

  289.           vcf=TNseq.TNseq_pass_vcf,

  290.           hg=hg,

  291.           annovar_database=annovar_database,

  292.           docker=annovar_docker,

  293.           cluster_config=cluster_config,

  294.           disk_size=disk_size

  295.         }

  296.       }

  297. 

  298.       if (vep) {

  299.         call VEP.VEP as TNseq_VEP {

  300.           input: 

  301.           vcf=TNseq.TNseq_pass_vcf,

  302.           hg=hg,

  303.           sample_id=sample_id,

  304.           tumor_id=sample_id + ".T",

  305.           normal_id=sample_id + ".N",

  306.           ref_dir=ref_dir,

  307.           fasta=fasta,

  308.           vep_path=vep_path,

  309.           cache=cache,

  310.           species=species,

  311.           vcf2maf_path=vcf2maf_path,

  312.           docker=vep_docker,

  313.           cluster_config=cluster_config,

  314.           disk_size=disk_size

  315.         }

  316.       }

  317.     }

  318. 

  319.     if (tnscope) {

  320.       call TNscope.TNscope as TNscope {

  321.         input:

  322.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  323.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  324.         sample=sample_id,

  325.         normal_recaled_bam=normal_BQSR.recaled_bam,

  326.         normal_recaled_bam_index=normal_BQSR.recaled_bam_index,

  327.         tumor_recaled_bam=tumor_BQSR.recaled_bam,

  328.         tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,

  329.         normal_name=sample_id + ".N",

  330.         tumor_name=sample_id + ".T",

  331.         fasta=fasta,

  332.         ref_dir=ref_dir,

  333.         regions=regions,

  334.         interval_padding=interval_padding,

  335.         dbsnp=dbsnp,

  336.         dbsnp_dir=dbsnp_dir,

  337.         pon_vcf=tnscope_pon,

  338.         docker=sentieon_docker,

  339.         cluster_config=cluster_config,

  340.         disk_size=disk_size

  341.       }

  342.       

  343.       if (annovar) {

  344.         call ANNOVAR.ANNOVAR as TNscope_annovar {

  345.           input:

  346.           vcf=TNscope.TNscope_pass_vcf,

  347.           hg=hg,

  348.           annovar_database=annovar_database,

  349.           docker=annovar_docker,

  350.           cluster_config=cluster_config,

  351.           disk_size=disk_size

  352.         }

  353.       }

  354. 

  355.       if (vep) {

  356.         call VEP.VEP as TNscope_VEP {

  357.           input: 

  358.           vcf=TNscope.TNscope_pass_vcf,

  359.           hg=hg,

  360.           sample_id=sample_id,

  361.           tumor_id=sample_id + ".T",

  362.           normal_id=sample_id + ".N",

  363.           ref_dir=ref_dir,

  364.           fasta=fasta,

  365.           vep_path=vep_path,

  366.           cache=cache,

  367.           species=species,

  368.           vcf2maf_path=vcf2maf_path,

  369.           docker=vep_docker,

  370.           cluster_config=cluster_config,

  371.           disk_size=disk_size

  372.         }

  373.       }

  374.     }

  375. 

  376.     if (varscan && normal_fastq_1 != "") {

  377.       call somatic.somatic as somatic {

  378.         input:

  379.         sample=sample_id,

  380.         normal_bam=normal_BQSR.recaled_bam,

  381.         normal_bam_index=normal_BQSR.recaled_bam_index,

  382.         tumor_bam=tumor_BQSR.recaled_bam,

  383.         tumor_bam_index=tumor_BQSR.recaled_bam_index,

  384.         ref_dir=ref_dir,

  385.         fasta=fasta,    

  386.         docker=varscan_docker,

  387.         disk_size=disk_size,

  388.         cluster_config=cluster_config

  389.       }

  390. 

  391.       call processSomatic.processSomatic as processSomatic {

  392.         input:

  393.         sample=sample_id,

  394.         varscan_snp=somatic.varscan_snp,

  395.         varscan_indel=somatic.varscan_indel,   

  396.         docker=varscan_docker,

  397.         disk_size=disk_size,

  398.         cluster_config=cluster_config

  399.       }

  400. 

  401.       call somaticFilter.somaticFilter as somaticFilter {

  402.         input:

  403.         sample=sample_id,

  404.         varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,

  405.         varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,

  406.         varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,

  407.         varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,

  408.         varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,

  409.         varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,

  410.         varscan_indel=somatic.varscan_indel,   

  411.         docker=varscan_docker,

  412.         disk_size=disk_size,

  413.         cluster_config=cluster_config

  414.       }

  415. 

  416.       if (annovar) {

  417.         call ANNOVAR.ANNOVAR as VarScan_annovar {

  418.           input:

  419.           vcf=somaticFilter.varscan_somatic_filter,

  420.           hg=hg,

  421.           annovar_database=annovar_database,

  422.           docker=annovar_docker,

  423.           cluster_config=cluster_config,

  424.           disk_size=disk_size

  425.         }

  426.       }

  427. 

  428.       if (vep) {

  429.         call VEP.VEP as VarScan_VEP {

  430.           input: 

  431.           vcf=somaticFilter.varscan_somatic_filter,

  432.           hg=hg,

  433.           sample_id=sample_id,

  434.           tumor_id=sample_id + ".T",

  435.           normal_id=sample_id + ".N",

  436.           ref_dir=ref_dir,

  437.           fasta=fasta,

  438.           vep_path=vep_path,

  439.           cache=cache,

  440.           species=species,

  441.           vcf2maf_path=vcf2maf_path,

  442.           docker=vep_docker,

  443.           cluster_config=cluster_config,

  444.           disk_size=disk_size

  445.         }

  446.       }

  447.     }

  448.   }

  449. 

  450.   if (input_bam) {

  451.     if (tumor_deduped_bam != "") {

  452.       call replaceRG.replaceRG as tumor_replaceRG {

  453.         input:

  454.         bam=tumor_deduped_bam,

  455.         group=sample_id + '.T',

  456.         sample=sample_id + '.T',

  457.         pl=pl,

  458.         docker=samtools_docker,

  459.         disk_size=disk_size,

  460.         cluster_config=cluster_config

  461.       }

  462.     }

  463.     

  464.     if (normal_deduped_bam != "") {

  465.       call replaceRG.replaceRG as normal_replaceRG {

  466.         input:

  467.         bam=normal_deduped_bam,

  468.         group=sample_id + '.N',

  469.         sample=sample_id + '.N',

  470.         pl=pl,

  471.         docker=samtools_docker,

  472.         disk_size=disk_size,

  473.         cluster_config=cluster_config

  474.       }

  475.     }

  476.     

  477.     if (haplotyper) {

  478.       call Haplotyper.Haplotyper as Haplotyper_fb {

  479.         input:

  480.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  481.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  482.         sample=sample_id + '.N',

  483.         fasta=fasta,

  484.         ref_dir=ref_dir,

  485.         recaled_bam=normal_BQSR_fb.recaled_bam,

  486.         recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  487.         dbsnp=dbsnp,

  488.         dbsnp_dir=dbsnp_dir,

  489.         regions=regions,

  490.         docker=sentieon_docker,

  491.         disk_size=disk_size,

  492.         cluster_config=cluster_config

  493.       }

  494.     }

  495. 

  496.     if (pindel) {

  497.       call Pindel.Pindel as Pindel_fb {

  498.         input:

  499.         sample_id=sample_id + '.N',

  500.         bam=normal_BQSR_fb.recaled_bam,

  501.         bam_index=normal_BQSR_fb.recaled_bam_index,

  502.         fasta=fasta,

  503.         ref_dir=ref_dir,

  504.         docker=pindel_docker,

  505.         disk_size=disk_size,

  506.         cluster_config=cluster_config

  507.       }

  508.     }

  509. 

  510.     if (tnseq) {

  511.       call TNseq.TNseq as TNseq_fb {

  512.         input:

  513.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  514.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  515.         sample=sample_id,

  516.         normal_recaled_bam=normal_BQSR_fb.recaled_bam,

  517.         normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  518.         tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,

  519.         tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,

  520.         normal_name=sample_id + ".N",

  521.         tumor_name=sample_id + ".T",

  522.         fasta=fasta,

  523.         ref_dir=ref_dir,

  524.         regions=regions,

  525.         interval_padding=interval_padding,

  526.         germline_resource=germline_resource,

  527.         germline_resource_tbi=germline_resource_tbi,

  528.         pon_vcf=tnseq_pon,

  529.         docker=sentieon_docker,

  530.         cluster_config=cluster_config,

  531.         disk_size=disk_size

  532.       }

  533. 

  534.       if (annovar) {

  535.         call ANNOVAR.ANNOVAR as TNseq_annovar_fb {

  536.           input:

  537.           vcf=TNseq_fb.TNseq_pass_vcf,

  538.           hg=hg,

  539.           annovar_database=annovar_database,

  540.           docker=annovar_docker,

  541.           cluster_config=cluster_config,

  542.           disk_size=disk_size

  543.         }

  544.       }

  545. 

  546.       if (vep) {

  547.         call VEP.VEP as TNseq_VEP_fb {

  548.           input: 

  549.           vcf=TNseq_fb.TNseq_pass_vcf,

  550.           hg=hg,

  551.           sample_id=sample_id,

  552.           tumor_id=sample_id + ".T",

  553.           normal_id=sample_id + ".N",

  554.           ref_dir=ref_dir,

  555.           fasta=fasta,

  556.           vep_path=vep_path,

  557.           cache=cache,

  558.           species=species,

  559.           vcf2maf_path=vcf2maf_path,

  560.           docker=vep_docker,

  561.           cluster_config=cluster_config,

  562.           disk_size=disk_size

  563.         }

  564.       }

  565.     }

  566. 

  567.     if (tnscope) {

  568.       call TNscope.TNscope as TNscope_fb {

  569.         input:

  570.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  571.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  572.         sample=sample_id,

  573.         normal_recaled_bam=normal_BQSR_fb.recaled_bam,

  574.         normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  575.         tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,

  576.         tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,

  577.         normal_name=sample_id + ".N",

  578.         tumor_name=sample_id + ".T",

  579.         fasta=fasta,

  580.         ref_dir=ref_dir,

  581.         regions=regions,

  582.         interval_padding=interval_padding,

  583.         dbsnp=dbsnp,

  584.         dbsnp_dir=dbsnp_dir,

  585.         pon_vcf=tnscope_pon,

  586.         docker=sentieon_docker,

  587.         cluster_config=cluster_config,

  588.         disk_size=disk_size

  589.       }

  590.       

  591.       if (annovar) {

  592.         call ANNOVAR.ANNOVAR as TNscope_annovar_fb {

  593.           input:

  594.           vcf=TNscope_fb.TNscope_pass_vcf,

  595.           hg=hg,

  596.           annovar_database=annovar_database,

  597.           docker=annovar_docker,

  598.           cluster_config=cluster_config,

  599.           disk_size=disk_size

  600.         }

  601.       }

  602. 

  603.       if (vep) {

  604.         call VEP.VEP as TNscope_VEP_fb {

  605.           input: 

  606.           vcf=TNscope_fb.TNscope_pass_vcf,

  607.           hg=hg,

  608.           sample_id=sample_id,

  609.           tumor_id=sample_id + ".T",

  610.           normal_id=sample_id + ".N",

  611.           ref_dir=ref_dir,

  612.           fasta=fasta,

  613.           vep_path=vep_path,

  614.           cache=cache,

  615.           species=species,

  616.           vcf2maf_path=vcf2maf_path,

  617.           docker=vep_docker,

  618.           cluster_config=cluster_config,

  619.           disk_size=disk_size

  620.         }

  621.       }

  622.     }

  623. 

  624.     if (varscan && normal_deduped_bam != "") {

  625.       call somatic.somatic as somatic_fb {

  626.         input:

  627.         sample=sample_id,

  628.         normal_bam=normal_BQSR_fb.recaled_bam,

  629.         normal_bam_index=normal_BQSR_fb.recaled_bam_index,

  630.         tumor_bam=tumor_BQSR_fb.recaled_bam,

  631.         tumor_bam_index=tumor_BQSR_fb.recaled_bam_index,

  632.         ref_dir=ref_dir,

  633.         fasta=fasta,    

  634.         docker=varscan_docker,

  635.         disk_size=disk_size,

  636.         cluster_config=cluster_config

  637.       }

  638. 

  639.       call processSomatic.processSomatic as processSomatic_fb {

  640.         input:

  641.         sample=sample_id,

  642.         varscan_snp=somatic_fb.varscan_snp,

  643.         varscan_indel=somatic_fb.varscan_indel,   

  644.         docker=varscan_docker,

  645.         disk_size=disk_size,

  646.         cluster_config=cluster_config

  647.       }

  648. 

  649.       call somaticFilter.somaticFilter as somaticFilter_fb {

  650.         input:

  651.         sample=sample_id,

  652.         varscan_snp_somatic_hc=processSomatic_fb.varscan_snp_somatic_hc,

  653.         varscan_snp_germline_hc=processSomatic_fb.varscan_snp_germline_hc,

  654.         varscan_snp_loh_hc=processSomatic_fb.varscan_snp_loh_hc,

  655.         varscan_indel_somatic_hc=processSomatic_fb.varscan_indel_somatic_hc,

  656.         varscan_indel_germline_hc=processSomatic_fb.varscan_indel_germline_hc,

  657.         varscan_indel_loh_hc=processSomatic_fb.varscan_indel_loh_hc,

  658.         varscan_indel=somatic_fb.varscan_indel,   

  659.         docker=varscan_docker,

  660.         disk_size=disk_size,

  661.         cluster_config=cluster_config

  662.       }

  663. 

  664.       if (annovar) {

  665.         call ANNOVAR.ANNOVAR as VarScan_annovar_fb {

  666.           input:

  667.           vcf=somaticFilter_fb.varscan_somatic_filter,

  668.           hg=hg,

  669.           annovar_database=annovar_database,

  670.           docker=annovar_docker,

  671.           cluster_config=cluster_config,

  672.           disk_size=disk_size

  673.         }

  674.       }

  675. 

  676.       if (vep) {

  677.         call VEP.VEP as VarScan_VEP_fb {

  678.           input: 

  679.           vcf=somaticFilter_fb.varscan_somatic_filter,

  680.           hg=hg,

  681.           sample_id=sample_id,

  682.           tumor_id=sample_id + ".T",

  683.           normal_id=sample_id + ".N",

  684.           ref_dir=ref_dir,

  685.           fasta=fasta,

  686.           vep_path=vep_path,

  687.           cache=cache,

  688.           species=species,

  689.           vcf2maf_path=vcf2maf_path,

  690.           docker=vep_docker,

  691.           cluster_config=cluster_config,

  692.           disk_size=disk_size

  693.         }

  694.       }

  695.     }

  696.   }

  697. }