run_PureCN#

Inputs#

Required#

  • genome (String, required)

  • intervals (File, required)

  • sampleID (String, required)

  • segFile (File, required)

  • vcf (File, required)

Defaults#

  • PureCN.funSegmentation (String, default=”Hclust”)

  • PureCN.hardware_disk_size_GB (Int, default=250)

  • PureCN.hardware_memory_GB (Int, default=32)

  • PureCN.hardware_preemptible_tries (Int, default=2)

  • PureCN.maxCopyNumber (Int, default=8)

  • PureCN.maxPurity (Float, default=0.99)

  • PureCN.maxSegments (Int, default=1000)

  • PureCN.max_retries (Int, default=0)

  • PureCN.minPurity (Float, default=0.9)

  • PureCN.num_threads (Int, default=1)

  • PureCN.otherArguments (String, default=”–post-optimize –model-homozygous –min-total-counts 20”)

  • PureCN.purecn_docker (String, default=”markusriester/purecn:2.2.0”)

Outputs#

  • solutions_pdf (File)

  • chromosomes_pdf (File)

  • rds (File)

  • dnacopy (File)

  • variants (File)

  • loh (File)

  • genes (File)

  • segmentation (File)

  • log (File)

  • selected_solution (File)

  • local_optima_pdf (File)

  • purity (String)

  • ploidy (String)

  • contamination (String)

  • flagged (String)

  • curated (String)

  • comment (String)

  • wgd (String)

  • loh_fraction (String)

  • cin (String)

  • cin_allele_specific (String)

  • cin_ploidy_robust (String)

  • cin_allele_specific_ploidy_robust (String)

PureCN#

Inputs#

Required#

  • intervals (File, required)

  • sampleID (String, required)

  • segFile (File, required)

  • vcf (File, required)

Defaults#

  • funSegmentation (String, default=”Hclust”)

  • genome (String, default=”hg38”)

  • hardware_disk_size_GB (Int, default=250)

  • hardware_memory_GB (Int, default=32)

  • hardware_preemptible_tries (Int, default=2)

  • maxCopyNumber (Int, default=8)

  • maxPurity (Float, default=0.99)

  • maxSegments (Int, default=1000)

  • max_retries (Int, default=0)

  • minPurity (Float, default=0.9)

  • num_threads (Int, default=1)

  • otherArguments (String, default=”–post-optimize –model-homozygous –min-total-counts 20”)

  • purecn_docker (String, default=”markusriester/purecn:2.2.0”)

Outputs#

  • solutions_pdf (File)

  • chromosomes_pdf (File)

  • rds (File)

  • dnacopy (File)

  • variants (File)

  • loh (File)

  • genes (File)

  • segmentation (File)

  • log (File)

  • selected_solution (File)

  • local_optima_pdf (File)

  • table (Array[String])

  • purity (String)

  • ploidy (String)

  • contamination (String)

  • flagged (String)

  • curated (String)

  • comment (String)

  • wgd_table (Array[String])

  • wgd (String)

  • loh_fraction (String)

  • cin (String)

  • cin_allele_specific (String)

  • cin_ploidy_robust (String)

  • cin_allele_specific_ploidy_robust (String)