WARNING: this workflow is experimental! Use at your own risk!

samtools_merge

description
Runs samtools merge, with optional iteration to avoid maximum command line argument length
outputs
{'merged_bam': 'The BAM resulting from merging all the input BAMs'}
allowNestedInputs
true

Inputs

Required

  • bams (Array[File], required): BAMs to merge into a final BAM
  • prefix (String, required): Prefix for output BAM.
  • basic_merge._runtime (Any, required)
  • final_merge._runtime (Any, required)
  • inner_merge._runtime (Any, required)

Optional

  • basic_merge.new_header (File?)
  • final_merge.new_header (File?)
  • inner_merge.new_header (File?)

Defaults

  • max_length (Int, default=100): Maximum number of BAMs to merge before using iteration
  • use_all_cores (Boolean, default=false): Use all cores? Recommended for cloud environments.
  • basic_merge.combine_rg (Boolean, default=true)
  • basic_merge.modify_disk_size_gb (Int, default=0)
  • basic_merge.name_sorted (Boolean, default=false)
  • basic_merge.ncpu (Int, default=2)
  • basic_merge.region (String, default="")
  • final_merge.modify_disk_size_gb (Int, default=0)
  • final_merge.name_sorted (Boolean, default=false)
  • final_merge.ncpu (Int, default=2)
  • final_merge.region (String, default="")
  • inner_merge.combine_rg (Boolean, default=true)
  • inner_merge.modify_disk_size_gb (Int, default=0)
  • inner_merge.name_sorted (Boolean, default=false)
  • inner_merge.ncpu (Int, default=2)
  • inner_merge.region (String, default="")

Outputs

  • merged_bam (File)