Longbow

Process

description
Process a BAM file using Longbow

Inputs

Required

  • bam (File, required): BAM file to process

Optional

  • barcode_allow_list (File?): File containing a list of barcodes to allow
  • barcode_tag (String?): Tag containing the barcode
  • corrected_tag (String?): Tag to use for corrected barcode
  • model (String?): Longbow model to use for processing
  • AggregateCorrectLogStats.runtime_attr_override (RuntimeAttr?)
  • Extract.bam_pbi (File?)
  • Extract.leading_adapter (String?)
  • Extract.runtime_attr_override (RuntimeAttr?)
  • Extract.start_offset (Int?)
  • Extract.trailing_adapter (String?)
  • t_01_Peek.runtime_attr_override (RuntimeAttr?)
  • t_02_Annotate.runtime_attr_override (RuntimeAttr?)
  • t_03_Filter.bam_pbi (File?)
  • t_03_Filter.model (String?): Longbow model to use for processing
  • t_03_Filter.runtime_attr_override (RuntimeAttr?)
  • t_04_Segment.model (String?): Longbow model to use for processing
  • t_04_Segment.runtime_attr_override (RuntimeAttr?)
  • t_05_RemoveMasSeqTruncatedReads.runtime_attr_override (RuntimeAttr?)
  • t_07_PadUMI.runtime_attr_override (RuntimeAttr?)
  • t_08_PadCBC.runtime_attr_override (RuntimeAttr?)
  • t_09_Correct.barcode_freq_list (File?)
  • t_09_Correct.runtime_attr_override (RuntimeAttr?)
  • t_10_AdjustUmiSequenceWithAdapterAlignment.runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out"): Prefix for output files
  • same_barcode_per_read (Boolean, default=false): Whether to assume that all reads in a pair have the same barcode
  • shard_width (Int, default=25): Width of shards to use for processing
  • Extract.base_padding (Int, default=2)
  • Extract.num_cpus (Int, default=2)
  • t_01_Peek.n (Int, default=100)
  • t_02_Annotate.num_cpus (Int, default=8)
  • t_03_Filter.num_cpus (Int, default=2)
  • t_04_Segment.num_cpus (Int, default=2)
  • t_07_PadUMI.padding (Int, default=2)
  • t_08_PadCBC.padding (Int, default=2)
  • t_09_Correct.ccs_lev_dist_threshold (Int, default=2)
  • t_09_Correct.clr_lev_dist_threshold (Int, default=2)
  • t_10_AdjustUmiSequenceWithAdapterAlignment.existing_umi_tag (String, default="ZU")
  • t_10_AdjustUmiSequenceWithAdapterAlignment.new_umi_tag (String, default="JX")

Outputs

  • annotated_bam (File)
  • segmented_bam (File)
  • filtered_bam (File)
  • filter_failed_bam (File)
  • corrected_bam (File?)
  • uncorrectable_bam (File?)
  • extracted_bam (File)
  • correct_stats (File?)
  • correct_log (File?)
  • umi_adjustment_log (File)

Dot Diagram

Longbow