renluyao
/
variant-calling
atdalīts no YaqingLiu/variant-calling
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Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
Nevar pievienot vairāk kā 25 tēmas Tēmai ir jāsākas ar burtu vai ciparu, tā var saturēt domu zīmes ('-') un var būt līdz 35 simboliem gara.
82 Revīzijas
1 Atzars
Koks: 33b1c80f3e
Atzari Tagi
${ item.name }
Izveidot atzaru ${ searchTerm }
no '33b1c80f3e'
${ noResults }
variant-calling/workflow.wdl

703 rindas
20KB
Neapstrādāts Vainot Vēsture 

  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.         deduped_bam=normal_Dedup.deduped_bam,

  235.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  236.         recal_table=normal_BQSR.recal_table,

  237.         dbsnp=dbsnp,

  238.         dbsnp_dir=dbsnp_dir,

  239.         regions=regions,

  240.         docker=sentieon_docker,

  241.         disk_size=disk_size,

  242.         cluster_config=cluster_config

  243.       }

  244.     }

  245.     

  246.     if (tnseq) {

  247.       call TNseq.TNseq as TNseq {

  248.         input:

  249.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  250.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  251.         sample=sample_id,

  252.         normal_deduped_bam=normal_Dedup.deduped_bam,

  253.         normal_deduped_bam_index=normal_Dedup.deduped_bam_index,

  254.         normal_recal_table=normal_BQSR.recal_table,

  255.         tumor_deduped_bam=tumor_Dedup.deduped_bam,

  256.         tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,

  257.         tumor_recal_table=tumor_BQSR.recal_table,

  258.         normal_name=sample_id + "_normal",

  259.         tumor_name=sample_id + "_tumor",

  260.         fasta=fasta,

  261.         ref_dir=ref_dir,

  262.         regions=regions,

  263.         interval_padding=interval_padding,

  264.         germline_resource=germline_resource,

  265.         germline_resource_tbi=germline_resource_tbi,

  266.         pon_vcf=tnseq_pon,

  267.         docker=sentieon_docker,

  268.         cluster_config=cluster_config,

  269.         disk_size=disk_size

  270.       }

  271. 

  272.       if (annovar) {

  273.         call ANNOVAR.ANNOVAR as TNseq_annovar {

  274.           input:

  275.           vcf=TNseq.TNseq_vcf,

  276.           hg=hg,

  277.           only_pass=only_pass,

  278.           annovar_database=annovar_database,

  279.           docker=annovar_docker,

  280.           cluster_config=cluster_config,

  281.           disk_size=disk_size

  282.         }

  283.       }

  284. 

  285.       if (vep) {

  286.         call VEP.VEP as TNseq_VEP {

  287.           input: 

  288.           vcf=TNseq.TNseq_vcf,

  289.           hg=hg,

  290.           only_pass=only_pass,

  291.           sample_id=sample_id,

  292.           tumor_id=sample_id + "_tumor",

  293.           normal_id=sample_id + "_normal",

  294.           ref_dir=ref_dir,

  295.           fasta=fasta,

  296.           vep_path=vep_path,

  297.           cache=cache,

  298.           species=species,

  299.           vcf2maf_path=vcf2maf_path,

  300.           docker=vep_docker,

  301.           cluster_config=cluster_config,

  302.           disk_size=disk_size

  303.         }

  304.       }

  305.     }

  306. 

  307.     if (tnscope) {

  308.       call TNscope.TNscope as TNscope {

  309.         input:

  310.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  311.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  312.         sample=sample_id,

  313.         normal_deduped_bam=normal_Dedup.deduped_bam,

  314.         normal_deduped_bam_index=normal_Dedup.deduped_bam_index,

  315.         normal_recal_table=normal_BQSR.recal_table,

  316.         tumor_deduped_bam=tumor_Dedup.deduped_bam,

  317.         tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,

  318.         tumor_recal_table=tumor_BQSR.recal_table,

  319.         normal_name=sample_id + "_normal",

  320.         tumor_name=sample_id + "_tumor",

  321.         fasta=fasta,

  322.         ref_dir=ref_dir,

  323.         regions=regions,

  324.         interval_padding=interval_padding,

  325.         dbsnp=dbsnp,

  326.         dbsnp_dir=dbsnp_dir,

  327.         pon_vcf=tnscope_pon,

  328.         docker=sentieon_docker,

  329.         cluster_config=cluster_config,

  330.         disk_size=disk_size

  331.       }

  332.       

  333.       if (annovar) {

  334.         call ANNOVAR.ANNOVAR as TNscope_annovar {

  335.           input:

  336.           vcf=TNscope.TNscope_vcf,

  337.           hg=hg,

  338.           only_pass=only_pass,

  339.           annovar_database=annovar_database,

  340.           docker=annovar_docker,

  341.           cluster_config=cluster_config,

  342.           disk_size=disk_size

  343.         }

  344.       }

  345. 

  346.       if (vep) {

  347.         call VEP.VEP as TNscope_VEP {

  348.           input: 

  349.           vcf=TNscope.TNscope_vcf,

  350.           hg=hg,

  351.           only_pass=only_pass,

  352.           sample_id=sample_id,

  353.           tumor_id=sample_id + "_tumor",

  354.           normal_id=sample_id + "_normal",

  355.           ref_dir=ref_dir,

  356.           fasta=fasta,

  357.           vep_path=vep_path,

  358.           cache=cache,

  359.           species=species,

  360.           vcf2maf_path=vcf2maf_path,

  361.           docker=vep_docker,

  362.           cluster_config=cluster_config,

  363.           disk_size=disk_size

  364.         }

  365.       }

  366.     }

  367. 

  368.     if (varscan) {

  369.       call somatic.somatic as somatic {

  370.         input:

  371.         sample=sample_id,

  372.         tumor_bam=tumor_Dedup.deduped_bam,

  373.         tumor_bam_index=tumor_Dedup.deduped_bam_index,

  374.         normal_bam=normal_Dedup.deduped_bam,

  375.         normal_bam_index=normal_Dedup.deduped_bam_index,

  376.         ref_dir=ref_dir,

  377.         fasta=fasta,    

  378.         docker=varscan_docker,

  379.         disk_size=disk_size,

  380.         cluster_config=cluster_config

  381.       }

  382. 

  383.       call processSomatic.processSomatic as processSomatic {

  384.         input:

  385.         sample=sample_id,

  386.         varscan_snp=somatic.varscan_snp,

  387.         varscan_indel=somatic.varscan_indel,   

  388.         docker=varscan_docker,

  389.         disk_size=disk_size,

  390.         cluster_config=cluster_config

  391.       }

  392. 

  393.       call somaticFilter.somaticFilter as somaticFilter {

  394.         input:

  395.         sample=sample_id,

  396.         varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,

  397.         varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,

  398.         varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,

  399.         varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,

  400.         varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,

  401.         varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,

  402.         varscan_indel=somatic.varscan_indel,   

  403.         docker=varscan_docker,

  404.         disk_size=disk_size,

  405.         cluster_config=cluster_config

  406.       }

  407. 

  408.       if (annovar) {

  409.         call ANNOVAR.ANNOVAR as VarScan_annovar {

  410.           input:

  411.           vcf=somaticFilter.varscan_somatic_filter,

  412.           hg=hg,

  413.           only_pass=only_pass,

  414.           annovar_database=annovar_database,

  415.           docker=annovar_docker,

  416.           cluster_config=cluster_config,

  417.           disk_size=disk_size

  418.         }

  419.       }

  420. 

  421.       if (vep) {

  422.         call VEP.VEP as VarScan_VEP {

  423.           input: 

  424.           vcf=VarScan.VarScan_vcf,

  425.           hg=hg,

  426.           only_pass=only_pass,

  427.           sample_id=sample_id,

  428.           tumor_id=sample_id + "_tumor",

  429.           normal_id=sample_id + "_normal",

  430.           ref_dir=ref_dir,

  431.           fasta=fasta,

  432.           vep_path=vep_path,

  433.           cache=cache,

  434.           species=species,

  435.           vcf2maf_path=vcf2maf_path,

  436.           docker=vep_docker,

  437.           cluster_config=cluster_config,

  438.           disk_size=disk_size

  439.         }

  440.       }

  441.     }

  442.   }

  443. 

  444. 

  445.   if (input_bam) {

  446.     if (tumor_deduped_bam != "") {

  447.       call BQSR.BQSR as tumor_BQSR {

  448.         input:

  449.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  450.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  451.         fasta=fasta,

  452.         ref_dir=ref_dir,

  453.         deduped_bam=tumor_deduped_bam,

  454.         deduped_bam_index=tumor_deduped_bam_index,

  455.         db_mills=db_mills,

  456.         dbmills_dir=dbmills_dir,

  457.         dbsnp=dbsnp,

  458.         dbsnp_dir=dbsnp_dir,

  459.         sample=sample_id + '_tumor',

  460.         docker=sentieon_docker,

  461.         disk_size=disk_size,

  462.         cluster_config=cluster_config

  463.       }

  464.     }

  465.     

  466.     if (normal_deduped_bam != "") {

  467.       call BQSR.BQSR as normal_BQSR {

  468.         input:

  469.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  470.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  471.         fasta=fasta,

  472.         ref_dir=ref_dir,

  473.         deduped_bam=normal_deduped_bam,

  474.         deduped_bam_index=normal_deduped_bam_index,

  475.         db_mills=db_mills,

  476.         dbmills_dir=dbmills_dir,

  477.         dbsnp=dbsnp,

  478.         dbsnp_dir=dbsnp_dir,

  479.         sample=sample_id + '_normal',

  480.         docker=sentieon_docker,

  481.         disk_size=disk_size,

  482.         cluster_config=cluster_config

  483.       }

  484.     }

  485.     

  486.     if (haplotyper) {

  487.       call Haplotyper.Haplotyper as Haplotyper {

  488.         input:

  489.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  490.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  491.         sample=sample_id + '_normal',

  492.         fasta=fasta,

  493.         ref_dir=ref_dir,

  494.         deduped_bam=normal_Dedup.deduped_bam,

  495.         deduped_bam_index=normal_Dedup.deduped_bam_index,

  496.         recal_table=normal_BQSR.recal_table,

  497.         dbsnp=dbsnp,

  498.         dbsnp_dir=dbsnp_dir,

  499.         regions=regions,

  500.         docker=sentieon_docker,

  501.         disk_size=disk_size,

  502.         cluster_config=cluster_config

  503.       }

  504.     }

  505.     

  506.     if (tnseq) {

  507.       call TNseq.TNseq as TNseq {

  508.         input:

  509.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  510.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  511.         sample=sample_id,

  512.         normal_deduped_bam=normal_Dedup.deduped_bam,

  513.         normal_deduped_bam_index=normal_Dedup.deduped_bam_index,

  514.         normal_recal_table=normal_BQSR.recal_table,

  515.         tumor_deduped_bam=tumor_Dedup.deduped_bam,

  516.         tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,

  517.         tumor_recal_table=tumor_BQSR.recal_table,

  518.         normal_name=sample_id + "_normal",

  519.         tumor_name=sample_id + "_tumor",

  520.         fasta=fasta,

  521.         ref_dir=ref_dir,

  522.         regions=regions,

  523.         interval_padding=interval_padding,

  524.         germline_resource=germline_resource,

  525.         germline_resource_tbi=germline_resource_tbi,

  526.         pon_vcf=tnseq_pon,

  527.         docker=sentieon_docker,

  528.         cluster_config=cluster_config,

  529.         disk_size=disk_size

  530.       }

  531. 

  532.       if (annovar) {

  533.         call ANNOVAR.ANNOVAR as TNseq_annovar {

  534.           input:

  535.           vcf=TNseq.TNseq_vcf,

  536.           hg=hg,

  537.           only_pass=only_pass,

  538.           annovar_database=annovar_database,

  539.           docker=annovar_docker,

  540.           cluster_config=cluster_config,

  541.           disk_size=disk_size

  542.         }

  543.       }

  544. 

  545.       if (vep) {

  546.         call VEP.VEP as TNseq_VEP {

  547.           input: 

  548.           vcf=TNseq.TNseq_vcf,

  549.           hg=hg,

  550.           only_pass=only_pass,

  551.           sample_id=sample_id,

  552.           tumor_id=sample_id + "_tumor",

  553.           normal_id=sample_id + "_normal",

  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 {

  569.         input:

  570.         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,

  571.         SENTIEON_LICENSE=SENTIEON_LICENSE,

  572.         sample=sample_id,

  573.         normal_deduped_bam=normal_Dedup.deduped_bam,

  574.         normal_deduped_bam_index=normal_Dedup.deduped_bam_index,

  575.         normal_recal_table=normal_BQSR.recal_table,

  576.         tumor_deduped_bam=tumor_Dedup.deduped_bam,

  577.         tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,

  578.         tumor_recal_table=tumor_BQSR.recal_table,

  579.         normal_name=sample_id + "_normal",

  580.         tumor_name=sample_id + "_tumor",

  581.         fasta=fasta,

  582.         ref_dir=ref_dir,

  583.         regions=regions,

  584.         interval_padding=interval_padding,

  585.         dbsnp=dbsnp,

  586.         dbsnp_dir=dbsnp_dir,

  587.         pon_vcf=tnscope_pon,

  588.         docker=sentieon_docker,

  589.         cluster_config=cluster_config,

  590.         disk_size=disk_size

  591.       }

  592.       

  593.       if (annovar) {

  594.         call ANNOVAR.ANNOVAR as TNscope_annovar {

  595.           input:

  596.           vcf=TNscope.TNscope_vcf,

  597.           hg=hg,

  598.           only_pass=only_pass,

  599.           annovar_database=annovar_database,

  600.           docker=annovar_docker,

  601.           cluster_config=cluster_config,

  602.           disk_size=disk_size

  603.         }

  604.       }

  605. 

  606.       if (vep) {

  607.         call VEP.VEP as TNscope_VEP {

  608.           input: 

  609.           vcf=TNscope.TNscope_vcf,

  610.           hg=hg,

  611.           only_pass=only_pass,

  612.           sample_id=sample_id,

  613.           tumor_id=sample_id + "_tumor",

  614.           normal_id=sample_id + "_normal",

  615.           ref_dir=ref_dir,

  616.           fasta=fasta,

  617.           vep_path=vep_path,

  618.           cache=cache,

  619.           species=species,

  620.           vcf2maf_path=vcf2maf_path,

  621.           docker=vep_docker,

  622.           cluster_config=cluster_config,

  623.           disk_size=disk_size

  624.         }

  625.       }

  626.     }

  627. 

  628.     if (varscan) {

  629.       call somatic.somatic as somatic {

  630.         input:

  631.         sample=sample_id,

  632.         tumor_bam=tumor_Dedup.deduped_bam,

  633.         tumor_bam_index=tumor_Dedup.deduped_bam_index,

  634.         normal_bam=normal_Dedup.deduped_bam,

  635.         normal_bam_index=normal_Dedup.deduped_bam_index,

  636.         ref_dir=ref_dir,

  637.         fasta=fasta,    

  638.         docker=varscan_docker,

  639.         disk_size=disk_size,

  640.         cluster_config=cluster_config

  641.       }

  642. 

  643.       call processSomatic.processSomatic as processSomatic {

  644.         input:

  645.         sample=sample_id,

  646.         varscan_snp=somatic.varscan_snp,

  647.         varscan_indel=somatic.varscan_indel,   

  648.         docker=varscan_docker,

  649.         disk_size=disk_size,

  650.         cluster_config=cluster_config

  651.       }

  652. 

  653.       call somaticFilter.somaticFilter as somaticFilter {

  654.         input:

  655.         sample=sample_id,

  656.         varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,

  657.         varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,

  658.         varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,

  659.         varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,

  660.         varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,

  661.         varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,

  662.         varscan_indel=somatic.varscan_indel,   

  663.         docker=varscan_docker,

  664.         disk_size=disk_size,

  665.         cluster_config=cluster_config

  666.       }

  667. 

  668.       if (annovar) {

  669.         call ANNOVAR.ANNOVAR as VarScan_annovar {

  670.           input:

  671.           vcf=somaticFilter.varscan_somatic_filter,

  672.           hg=hg,

  673.           only_pass=only_pass,

  674.           annovar_database=annovar_database,

  675.           docker=annovar_docker,

  676.           cluster_config=cluster_config,

  677.           disk_size=disk_size

  678.         }

  679.       }

  680. 

  681.       if (vep) {

  682.         call VEP.VEP as VarScan_VEP {

  683.           input: 

  684.           vcf=VarScan.VarScan_vcf,

  685.           hg=hg,

  686.           only_pass=only_pass,

  687.           sample_id=sample_id,

  688.           tumor_id=sample_id + "_tumor",

  689.           normal_id=sample_id + "_normal",

  690.           ref_dir=ref_dir,

  691.           fasta=fasta,

  692.           vep_path=vep_path,

  693.           cache=cache,

  694.           species=species,

  695.           vcf2maf_path=vcf2maf_path,

  696.           docker=vep_docker,

  697.           cluster_config=cluster_config,

  698.           disk_size=disk_size

  699.         }

  700.       }

  701.     }

  702.   }

  703. }