AlignReads

Minimap2

descrpiton
A wrapper to minimap2 for mapping & aligning (groups of) sequences to a reference

Inputs

Required

  • RG (String, required): read group information to be supplied to parameter '-R' (note that tabs should be input as ' ')
  • map_preset (String, required): preset to be used for minimap2 parameter '-x'
  • reads (Array[File], required): query sequences to be mapped and aligned
  • ref_fasta (File, required): reference fasta

Optional

  • library (String?)
  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out"): [default-valued] prefix for output BAM
  • tags_to_preserve (Array[String], default=[]): sam tags to carry over to aligned bam file

Outputs

  • aligned_bam (File)
  • aligned_bai (File)