run_vcf_to_depmap#

Inputs#

Required#

  • input_vcf (File, required)

  • sample_id (String, required)

Defaults#

  • vcf_to_depmap.boot_disk_size (Int, default=10)

  • vcf_to_depmap.cpu (Int, default=4)

  • vcf_to_depmap.disk_space (Int, default=40)

  • vcf_to_depmap.docker_image (String, default=”depmapomics:test”)

  • vcf_to_depmap.force_keep (Array[String], default=[‘oc_brca1_func_assay__class’, ‘oc_brca1_func_assay__score’, ‘clinvar_vcf_ssr’, ‘clinvar_vcf_clndisdbincl’, ‘clinvar_vcf_clnsigincl’, ‘clinvar_vcf_clndnincl’, ‘oc_oncokb__all’, ‘oc_oncokb__highestdiagnosticimplicationlevel’, ‘cgc_other_germline_mut’, ‘cgc_other_syndrome/disease’, ‘clinvar_vcf_clnsigconf’, ‘center’, ‘cosmicfusion_fusion_id’, ‘tumor_barcode’, ‘source”’, ‘clinvar_vcf_filter’, ‘clinvar_vcf_dbvarid’, ‘normal_barcode’, ‘gencode_34_ncbibuild’, ‘oc_oncokb_dm__highestprognosticimplicationlevel’, ‘strandq’, ‘oc_oncokb_dm__highestsensitivelevel’, ‘ocm’, ‘oc_oncokb_dm__all’, ‘seqq’, ‘nlod’, ‘contq’, ‘nalod’, ‘oc_base__note’, ‘oc_cancer_hotspots__samples’, ‘oc_oncokb_dm__highestresistancelevel’, ‘oc_oncokb_dm__tumorsummary’, ‘oc_oncokb_dm__highestdiagnosticimplicationlevel’, ‘oc_hess_drivers__signature’, ‘oc_hess_drivers__is_driver’])

  • vcf_to_depmap.mem (Int, default=32)

  • vcf_to_depmap.n_rows (Int, default=100000)

  • vcf_to_depmap.preemptible (Int, default=3)

  • vcf_to_depmap.use_multi (Boolean, default=false)

  • vcf_to_depmap.whitelist (Boolean, default=false)

Outputs#

  • full_file (Array[File])

  • depmap_maf (File)

vcf_to_depmap#

Inputs#

Required#

  • input_vcf (File, required)

  • sample_id (String, required)

Defaults#

  • boot_disk_size (Int, default=10)

  • cpu (Int, default=4)

  • disk_space (Int, default=40)

  • docker_image (String, default=”depmapomics:test”)

  • force_keep (Array[String], default=[‘oc_brca1_func_assay__class’, ‘oc_brca1_func_assay__score’, ‘clinvar_vcf_ssr’, ‘clinvar_vcf_clndisdbincl’, ‘clinvar_vcf_clnsigincl’, ‘clinvar_vcf_clndnincl’, ‘oc_oncokb__all’, ‘oc_oncokb__highestdiagnosticimplicationlevel’, ‘cgc_other_germline_mut’, ‘cgc_other_syndrome/disease’, ‘clinvar_vcf_clnsigconf’, ‘center’, ‘cosmicfusion_fusion_id’, ‘tumor_barcode’, ‘source”’, ‘clinvar_vcf_filter’, ‘clinvar_vcf_dbvarid’, ‘normal_barcode’, ‘gencode_34_ncbibuild’, ‘oc_oncokb_dm__highestprognosticimplicationlevel’, ‘strandq’, ‘oc_oncokb_dm__highestsensitivelevel’, ‘ocm’, ‘oc_oncokb_dm__all’, ‘seqq’, ‘nlod’, ‘contq’, ‘nalod’, ‘oc_base__note’, ‘oc_cancer_hotspots__samples’, ‘oc_oncokb_dm__highestresistancelevel’, ‘oc_oncokb_dm__tumorsummary’, ‘oc_oncokb_dm__highestdiagnosticimplicationlevel’, ‘oc_hess_drivers__signature’, ‘oc_hess_drivers__is_driver’])

  • mem (Int, default=32)

  • n_rows (Int, default=100000)

  • preemptible (Int, default=3)

  • use_multi (Boolean, default=false)

  • whitelist (Boolean, default=false)

Outputs#

  • full_file (Array[File])

  • depmap_maf (File)