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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/ANNOVAR.wdl" as ANNOVAR

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

  14. 

  15. 

  16. workflow {{ project_name }} {

  17.   

  18.   String sample_id

  19.   File? tumor_fastq_1

  20.   File? tumor_fastq_2

  21.   File? normal_fastq_1

  22.   File? normal_fastq_2

  23.   File? tumor_deduped_bam

  24.   File? tumor_deduped_bam_index

  25.   File? normal_deduped_bam

  26.   File? normal_deduped_bam_index

  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 annovar_docker

  36.   String vep_docker

  37. 

  38.   File ref_dir

  39.   String fasta

  40.   File dbmills_dir

  41.   String db_mills

  42.   File dbsnp_dir

  43.   String dbsnp

  44.   File germline_resource

  45.   File germline_resource_tbi

  46.   String hg

  47.   File annovar_database

  48.   

  49.   File? regions

  50.   Int? interval_padding

  51.   File? tnseq_pon

  52.   File? tnscope_pon

  53. 

  54.   String vep_path

  55.   File cache

  56.   String species

  57.   String vcf2maf_path

  58. 

  59.   String disk_size

  60.   String cluster_config

  61. 

  62.   Boolean haplotyper

  63.   Boolean tnseq

  64.   Boolean tnscope

  65.   Boolean varscan

  66. 

  67.   Boolean annovar

  68.   Boolean vep

  69.   Boolean only_pass

  70. 

  71.   if (input_fastq) {

  72.     if (tumor_fastq_1!= "") {

  73.       call mapping.mapping as tumor_mapping {

  74.         input: 

  75.         group=sample_id + '_tumor',

  76.         sample=sample_id + '_tumor',

  77.         fastq_1=tumor_fastq_1,

  78.         fastq_2=tumor_fastq_2,

  79.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  80.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  81.         pl="ILLUMINAL",

  82.         fasta=fasta,

  83.         ref_dir=ref_dir,

  84.         docker=sentieon_docker,

  85.         disk_size=disk_size,

  86.         cluster_config=cluster_config

  87.       }

  88. 

  89.       call Metrics.Metrics as tumor_Metrics {

  90.         input:

  91.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  92.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  93.         fasta=fasta,

  94.         ref_dir=ref_dir,

  95.         sorted_bam=tumor_mapping.sorted_bam,

  96.         sorted_bam_index=tumor_mapping.sorted_bam_index,

  97.         sample=sample_id + '_tumor',

  98.         docker=sentieon_docker,

  99.         disk_size=disk_size,

  100.         cluster_config=cluster_config

  101.       }

  102. 

  103.       call Dedup.Dedup as tumor_Dedup {

  104.         input:

  105.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  106.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  107.         sorted_bam=tumor_mapping.sorted_bam,

  108.         sorted_bam_index=tumor_mapping.sorted_bam_index,

  109.         sample=sample_id + '_tumor',

  110.         docker=sentieon_docker,

  111.         disk_size=disk_size,

  112.         cluster_config=cluster_config

  113.       }

  114. 

  115.       call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {

  116.         input:

  117.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  118.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  119.         fasta=fasta,

  120.         ref_dir=ref_dir,

  121.         deduped_bam=tumor_Dedup.deduped_bam,

  122.         deduped_bam_index=tumor_Dedup.deduped_bam_index,

  123.         sample=sample_id + '_tumor',

  124.         docker=sentieon_docker,

  125.         disk_size=disk_size,

  126.         cluster_config=cluster_config

  127.       }

  128. 

  129.       call BQSR.BQSR as tumor_BQSR {

  130.         input:

  131.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  132.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  133.         fasta=fasta,

  134.         ref_dir=ref_dir,

  135.         deduped_bam=tumor_Dedup.deduped_bam,

  136.         deduped_bam_index=tumor_Dedup.deduped_bam_index,

  137.         db_mills=db_mills,

  138.         dbmills_dir=dbmills_dir,

  139.         dbsnp=dbsnp,

  140.         dbsnp_dir=dbsnp_dir,

  141.         sample=sample_id + '_tumor',

  142.         docker=sentieon_docker,

  143.         disk_size=disk_size,

  144.         cluster_config=cluster_config

  145.       }

  146.     }

  147.     

  148.     if (normal_fastq_1!= "") {

  149.       call mapping.mapping as normal_mapping {

  150.         input: 

  151.         group=sample_id + '_normal',

  152.         sample=sample_id + '_normal',

  153.         fastq_1=normal_fastq_1,

  154.         fastq_2=normal_fastq_2,

  155.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  156.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  157.         pl="ILLUMINAL",

  158.         fasta=fasta,

  159.         ref_dir=ref_dir,

  160.         docker=sentieon_docker,

  161.         disk_size=disk_size,

  162.         cluster_config=cluster_config

  163.       }

  164. 

  165.       call Metrics.Metrics as normal_Metrics {

  166.         input:

  167.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  168.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  169.         fasta=fasta,

  170.         ref_dir=ref_dir,

  171.         sorted_bam=normal_mapping.sorted_bam,

  172.         sorted_bam_index=normal_mapping.sorted_bam_index,

  173.         sample=sample_id + '_normal',

  174.         regions=regions,

  175.         docker=sentieon_docker,

  176.         disk_size=disk_size,

  177.         cluster_config=cluster_config

  178.       }

  179. 

  180.       call Dedup.Dedup as normal_Dedup {

  181.         input:

  182.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  183.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  184.         sorted_bam=normal_mapping.sorted_bam,

  185.         sorted_bam_index=normal_mapping.sorted_bam_index,

  186.         sample=sample_id + '_normal',

  187.         docker=sentieon_docker,

  188.         disk_size=disk_size,

  189.         cluster_config=cluster_config

  190.       }

  191. 

  192.       call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {

  193.         input:

  194.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  195.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  196.         fasta=fasta,

  197.         ref_dir=ref_dir,

  198.         deduped_bam=normal_Dedup.deduped_bam,

  199.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  200.         sample=sample_id + '_normal',

  201.         regions=regions,

  202.         docker=sentieon_docker,

  203.         disk_size=disk_size,

  204.         cluster_config=cluster_config

  205.       }

  206. 

  207.       call BQSR.BQSR as normal_BQSR {

  208.         input:

  209.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  210.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  211.         fasta=fasta,

  212.         ref_dir=ref_dir,

  213.         deduped_bam=normal_Dedup.deduped_bam,

  214.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  215.         db_mills=db_mills,

  216.         dbmills_dir=dbmills_dir,

  217.         dbsnp=dbsnp,

  218.         dbsnp_dir=dbsnp_dir,

  219.         sample=sample_id + '_normal',

  220.         docker=sentieon_docker,

  221.         disk_size=disk_size,

  222.         cluster_config=cluster_config

  223.       }

  224.     }

  225.     

  226.     if (haplotyper) {

  227.       call Haplotyper.Haplotyper as Haplotyper {

  228.         input:

  229.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  230.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  231.         sample=sample_id + '_normal',

  232.         fasta=fasta,

  233.         ref_dir=ref_dir,

  234.         recaled_bam=normal_BQSR.recaled_bam,

  235.         recaled_bam_index=normal_BQSR.recaled_bam_index,

  236.         dbsnp=dbsnp,

  237.         dbsnp_dir=dbsnp_dir,

  238.         regions=regions,

  239.         docker=sentieon_docker,

  240.         disk_size=disk_size,

  241.         cluster_config=cluster_config

  242.       }

  243.     }

  244.     

  245.     if (tnseq) {

  246.       call TNseq.TNseq as TNseq {

  247.         input:

  248.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  249.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  250.         sample=sample_id,

  251.         normal_recaled_bam=normal_BQSR.recaled_bam,

  252.         normal_recaled_bam_index=normal_BQSR.recaled_bam_index,

  253.         tumor_recaled_bam=tumor_BQSR.recaled_bam,

  254.         tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,

  255.         normal_name=sample_id + "_normal",

  256.         tumor_name=sample_id + "_tumor",

  257.         fasta=fasta,

  258.         ref_dir=ref_dir,

  259.         regions=regions,

  260.         interval_padding=interval_padding,

  261.         germline_resource=germline_resource,

  262.         germline_resource_tbi=germline_resource_tbi,

  263.         pon_vcf=tnseq_pon,

  264.         docker=sentieon_docker,

  265.         cluster_config=cluster_config,

  266.         disk_size=disk_size

  267.       }

  268. 

  269.       if (annovar) {

  270.         call ANNOVAR.ANNOVAR as TNseq_annovar {

  271.           input:

  272.           vcf=TNseq.TNseq_filter_vcf,

  273.           hg=hg,

  274.           only_pass=only_pass,

  275.           annovar_database=annovar_database,

  276.           docker=annovar_docker,

  277.           cluster_config=cluster_config,

  278.           disk_size=disk_size

  279.         }

  280.       }

  281. 

  282.       if (vep) {

  283.         call VEP.VEP as TNseq_VEP {

  284.           input: 

  285.           vcf=TNseq.TNseq_filter_vcf,

  286.           hg=hg,

  287.           only_pass=only_pass,

  288.           sample_id=sample_id,

  289.           tumor_id=sample_id + "_tumor",

  290.           normal_id=sample_id + "_normal",

  291.           ref_dir=ref_dir,

  292.           fasta=fasta,

  293.           vep_path=vep_path,

  294.           cache=cache,

  295.           species=species,

  296.           vcf2maf_path=vcf2maf_path,

  297.           docker=vep_docker,

  298.           cluster_config=cluster_config,

  299.           disk_size=disk_size

  300.         }

  301.       }

  302.     }

  303. 

  304.     if (tnscope) {

  305.       call TNscope.TNscope as TNscope {

  306.         input:

  307.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  308.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  309.         sample=sample_id,

  310.         normal_recaled_bam=normal_BQSR.recaled_bam,

  311.         normal_recaled_bam_index=normal_BQSR.recaled_bam_index,

  312.         tumor_recaled_bam=tumor_BQSR.recaled_bam,

  313.         tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,

  314.         normal_name=sample_id + "_normal",

  315.         tumor_name=sample_id + "_tumor",

  316.         fasta=fasta,

  317.         ref_dir=ref_dir,

  318.         regions=regions,

  319.         interval_padding=interval_padding,

  320.         dbsnp=dbsnp,

  321.         dbsnp_dir=dbsnp_dir,

  322.         pon_vcf=tnscope_pon,

  323.         docker=sentieon_docker,

  324.         cluster_config=cluster_config,

  325.         disk_size=disk_size

  326.       }

  327.       

  328.       if (annovar) {

  329.         call ANNOVAR.ANNOVAR as TNscope_annovar {

  330.           input:

  331.           vcf=TNscope.TNscope_vcf,

  332.           hg=hg,

  333.           only_pass=only_pass,

  334.           annovar_database=annovar_database,

  335.           docker=annovar_docker,

  336.           cluster_config=cluster_config,

  337.           disk_size=disk_size

  338.         }

  339.       }

  340. 

  341.       if (vep) {

  342.         call VEP.VEP as TNscope_VEP {

  343.           input: 

  344.           vcf=TNscope.TNscope_vcf,

  345.           hg=hg,

  346.           only_pass=only_pass,

  347.           sample_id=sample_id,

  348.           tumor_id=sample_id + "_tumor",

  349.           normal_id=sample_id + "_normal",

  350.           ref_dir=ref_dir,

  351.           fasta=fasta,

  352.           vep_path=vep_path,

  353.           cache=cache,

  354.           species=species,

  355.           vcf2maf_path=vcf2maf_path,

  356.           docker=vep_docker,

  357.           cluster_config=cluster_config,

  358.           disk_size=disk_size

  359.         }

  360.       }

  361.     }

  362. 

  363.     if (varscan) {

  364.       call somatic.somatic as somatic {

  365.         input:

  366.         sample=sample_id,

  367.         normal_bam=normal_BQSR.recaled_bam,

  368.         normal_bam_index=normal_BQSR.recaled_bam_index,

  369.         tumor_bam=tumor_BQSR.recaled_bam,

  370.         tumor_bam_index=tumor_BQSR.recaled_bam_index,

  371.         ref_dir=ref_dir,

  372.         fasta=fasta,    

  373.         docker=varscan_docker,

  374.         disk_size=disk_size,

  375.         cluster_config=cluster_config

  376.       }

  377. 

  378.       call processSomatic.processSomatic as processSomatic {

  379.         input:

  380.         sample=sample_id,

  381.         varscan_snp=somatic.varscan_snp,

  382.         varscan_indel=somatic.varscan_indel,   

  383.         docker=varscan_docker,

  384.         disk_size=disk_size,

  385.         cluster_config=cluster_config

  386.       }

  387. 

  388.       call somaticFilter.somaticFilter as somaticFilter {

  389.         input:

  390.         sample=sample_id,

  391.         varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,

  392.         varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,

  393.         varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,

  394.         varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,

  395.         varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,

  396.         varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,

  397.         varscan_indel=somatic.varscan_indel,   

  398.         docker=varscan_docker,

  399.         disk_size=disk_size,

  400.         cluster_config=cluster_config

  401.       }

  402. 

  403.       if (annovar) {

  404.         call ANNOVAR.ANNOVAR as VarScan_annovar {

  405.           input:

  406.           vcf=somaticFilter.varscan_somatic_filter,

  407.           hg=hg,

  408.           only_pass=only_pass,

  409.           annovar_database=annovar_database,

  410.           docker=annovar_docker,

  411.           cluster_config=cluster_config,

  412.           disk_size=disk_size

  413.         }

  414.       }

  415. 

  416.       if (vep) {

  417.         call VEP.VEP as VarScan_VEP {

  418.           input: 

  419.           vcf=somaticFilter.varscan_somatic_filter,

  420.           hg=hg,

  421.           only_pass=only_pass,

  422.           sample_id=sample_id,

  423.           tumor_id=sample_id + "_tumor",

  424.           normal_id=sample_id + "_normal",

  425.           ref_dir=ref_dir,

  426.           fasta=fasta,

  427.           vep_path=vep_path,

  428.           cache=cache,

  429.           species=species,

  430.           vcf2maf_path=vcf2maf_path,

  431.           docker=vep_docker,

  432.           cluster_config=cluster_config,

  433.           disk_size=disk_size

  434.         }

  435.       }

  436.     }

  437.   }

  438. 

  439. 

  440.   if (input_bam) {

  441.     if (tumor_deduped_bam != "") {

  442.       call BQSR.BQSR as tumor_BQSR_fb {

  443.         input:

  444.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  445.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  446.         fasta=fasta,

  447.         ref_dir=ref_dir,

  448.         deduped_bam=tumor_deduped_bam,

  449.         deduped_bam_index=tumor_deduped_bam_index,

  450.         db_mills=db_mills,

  451.         dbmills_dir=dbmills_dir,

  452.         dbsnp=dbsnp,

  453.         dbsnp_dir=dbsnp_dir,

  454.         sample=sample_id + '_tumor',

  455.         docker=sentieon_docker,

  456.         disk_size=disk_size,

  457.         cluster_config=cluster_config

  458.       }

  459.     }

  460.     

  461.     if (normal_deduped_bam != "") {

  462.       call BQSR.BQSR as normal_BQSR_fb {

  463.         input:

  464.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  465.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  466.         fasta=fasta,

  467.         ref_dir=ref_dir,

  468.         deduped_bam=normal_deduped_bam,

  469.         deduped_bam_index=normal_deduped_bam_index,

  470.         db_mills=db_mills,

  471.         dbmills_dir=dbmills_dir,

  472.         dbsnp=dbsnp,

  473.         dbsnp_dir=dbsnp_dir,

  474.         sample=sample_id + '_normal',

  475.         docker=sentieon_docker,

  476.         disk_size=disk_size,

  477.         cluster_config=cluster_config

  478.       }

  479.     }

  480.     

  481.     if (haplotyper) {

  482.       call Haplotyper.Haplotyper as Haplotyper_fb {

  483.         input:

  484.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  485.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  486.         sample=sample_id + '_normal',

  487.         fasta=fasta,

  488.         ref_dir=ref_dir,

  489.         recaled_bam=normal_BQSR_fb.recaled_bam,

  490.         recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  491.         dbsnp=dbsnp,

  492.         dbsnp_dir=dbsnp_dir,

  493.         regions=regions,

  494.         docker=sentieon_docker,

  495.         disk_size=disk_size,

  496.         cluster_config=cluster_config

  497.       }

  498.     }

  499.     

  500.     if (tnseq) {

  501.       call TNseq.TNseq as TNseq_fb {

  502.         input:

  503.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  504.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  505.         sample=sample_id,

  506.         normal_recaled_bam=normal_BQSR_fb.recaled_bam,

  507.         normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  508.         tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,

  509.         tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,

  510.         normal_name=sample_id + "_normal",

  511.         tumor_name=sample_id + "_tumor",

  512.         fasta=fasta,

  513.         ref_dir=ref_dir,

  514.         regions=regions,

  515.         interval_padding=interval_padding,

  516.         germline_resource=germline_resource,

  517.         germline_resource_tbi=germline_resource_tbi,

  518.         pon_vcf=tnseq_pon,

  519.         docker=sentieon_docker,

  520.         cluster_config=cluster_config,

  521.         disk_size=disk_size

  522.       }

  523. 

  524.       if (annovar) {

  525.         call ANNOVAR.ANNOVAR as TNseq_annovar_fb {

  526.           input:

  527.           vcf=TNseq_fb.TNseq_filter_vcf,

  528.           hg=hg,

  529.           only_pass=only_pass,

  530.           annovar_database=annovar_database,

  531.           docker=annovar_docker,

  532.           cluster_config=cluster_config,

  533.           disk_size=disk_size

  534.         }

  535.       }

  536. 

  537.       if (vep) {

  538.         call VEP.VEP as TNseq_VEP_fb {

  539.           input: 

  540.           vcf=TNseq_fb.TNseq_filter_vcf,

  541.           hg=hg,

  542.           only_pass=only_pass,

  543.           sample_id=sample_id,

  544.           tumor_id=sample_id + "_tumor",

  545.           normal_id=sample_id + "_normal",

  546.           ref_dir=ref_dir,

  547.           fasta=fasta,

  548.           vep_path=vep_path,

  549.           cache=cache,

  550.           species=species,

  551.           vcf2maf_path=vcf2maf_path,

  552.           docker=vep_docker,

  553.           cluster_config=cluster_config,

  554.           disk_size=disk_size

  555.         }

  556.       }

  557.     }

  558. 

  559.     if (tnscope) {

  560.       call TNscope.TNscope as TNscope_fb {

  561.         input:

  562.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  563.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  564.         sample=sample_id,

  565.         normal_recaled_bam=normal_BQSR_fb.recaled_bam,

  566.         normal_recaled_bam_index=normal_BQSR_fb.recaled_bam_index,

  567.         tumor_recaled_bam=tumor_BQSR_fb.recaled_bam,

  568.         tumor_recaled_bam_index=tumor_BQSR_fb.recaled_bam_index,

  569.         normal_name=sample_id + "_normal",

  570.         tumor_name=sample_id + "_tumor",

  571.         fasta=fasta,

  572.         ref_dir=ref_dir,

  573.         regions=regions,

  574.         interval_padding=interval_padding,

  575.         dbsnp=dbsnp,

  576.         dbsnp_dir=dbsnp_dir,

  577.         pon_vcf=tnscope_pon,

  578.         docker=sentieon_docker,

  579.         cluster_config=cluster_config,

  580.         disk_size=disk_size

  581.       }

  582.       

  583.       if (annovar) {

  584.         call ANNOVAR.ANNOVAR as TNscope_annovar_fb {

  585.           input:

  586.           vcf=TNscope_fb.TNscope_vcf,

  587.           hg=hg,

  588.           only_pass=only_pass,

  589.           annovar_database=annovar_database,

  590.           docker=annovar_docker,

  591.           cluster_config=cluster_config,

  592.           disk_size=disk_size

  593.         }

  594.       }

  595. 

  596.       if (vep) {

  597.         call VEP.VEP as TNscope_VEP_fb {

  598.           input: 

  599.           vcf=TNscope_fb.TNscope_vcf,

  600.           hg=hg,

  601.           only_pass=only_pass,

  602.           sample_id=sample_id,

  603.           tumor_id=sample_id + "_tumor",

  604.           normal_id=sample_id + "_normal",

  605.           ref_dir=ref_dir,

  606.           fasta=fasta,

  607.           vep_path=vep_path,

  608.           cache=cache,

  609.           species=species,

  610.           vcf2maf_path=vcf2maf_path,

  611.           docker=vep_docker,

  612.           cluster_config=cluster_config,

  613.           disk_size=disk_size

  614.         }

  615.       }

  616.     }

  617. 

  618.     if (varscan) {

  619.       call somatic.somatic as somatic_fb {

  620.         input:

  621.         sample=sample_id,

  622.         normal_bam=normal_BQSR_fb.recaled_bam,

  623.         normal_bam_index=normal_BQSR_fb.recaled_bam_index,

  624.         tumor_bam=tumor_BQSR_fb.recaled_bam,

  625.         tumor_bam_index=tumor_BQSR_fb.recaled_bam_index,

  626.         ref_dir=ref_dir,

  627.         fasta=fasta,    

  628.         docker=varscan_docker,

  629.         disk_size=disk_size,

  630.         cluster_config=cluster_config

  631.       }

  632. 

  633.       call processSomatic.processSomatic as processSomatic_fb {

  634.         input:

  635.         sample=sample_id,

  636.         varscan_snp=somatic_fb.varscan_snp,

  637.         varscan_indel=somatic_fb.varscan_indel,   

  638.         docker=varscan_docker,

  639.         disk_size=disk_size,

  640.         cluster_config=cluster_config

  641.       }

  642. 

  643.       call somaticFilter.somaticFilter as somaticFilter_fb {

  644.         input:

  645.         sample=sample_id,

  646.         varscan_snp_somatic_hc=processSomatic_fb.varscan_snp_somatic_hc,

  647.         varscan_snp_germline_hc=processSomatic_fb.varscan_snp_germline_hc,

  648.         varscan_snp_loh_hc=processSomatic_fb.varscan_snp_loh_hc,

  649.         varscan_indel_somatic_hc=processSomatic_fb.varscan_indel_somatic_hc,

  650.         varscan_indel_germline_hc=processSomatic_fb.varscan_indel_germline_hc,

  651.         varscan_indel_loh_hc=processSomatic_fb.varscan_indel_loh_hc,

  652.         varscan_indel=somatic_fb.varscan_indel,   

  653.         docker=varscan_docker,

  654.         disk_size=disk_size,

  655.         cluster_config=cluster_config

  656.       }

  657. 

  658.       if (annovar) {

  659.         call ANNOVAR.ANNOVAR as VarScan_annovar_fb {

  660.           input:

  661.           vcf=somaticFilter_fb.varscan_somatic_filter,

  662.           hg=hg,

  663.           only_pass=only_pass,

  664.           annovar_database=annovar_database,

  665.           docker=annovar_docker,

  666.           cluster_config=cluster_config,

  667.           disk_size=disk_size

  668.         }

  669.       }

  670. 

  671.       if (vep) {

  672.         call VEP.VEP as VarScan_VEP_fb {

  673.           input: 

  674.           vcf=somaticFilter_fb.varscan_somatic_filter,

  675.           hg=hg,

  676.           only_pass=only_pass,

  677.           sample_id=sample_id,

  678.           tumor_id=sample_id + "_tumor",

  679.           normal_id=sample_id + "_normal",

  680.           ref_dir=ref_dir,

  681.           fasta=fasta,

  682.           vep_path=vep_path,

  683.           cache=cache,

  684.           species=species,

  685.           vcf2maf_path=vcf2maf_path,

  686.           docker=vep_docker,

  687.           cluster_config=cluster_config,

  688.           disk_size=disk_size

  689.         }

  690.       }

  691.     }

  692.   }

  693. }