RemoveSingleOrganismContamination

RemoveSingleOrganismContamination

author
Jonn Smith
description
A workflow to remove contamination originating from a single organism from a dataset.

Inputs

Required

  • LB (String, required): the value to place in the BAM read group's LB (library) field
  • SM (String, required): the value to place in the BAM read group's SM field
  • contaminant_ref_map_file (File, required): Table indicating reference sequence and auxillary file locations.
  • contaminant_ref_name (String, required): Name of the contaminant genome to be used in output files.
  • dir_prefix (String, required): directory prefix for output files

Optional

  • fq_end1 (File?): GCS path to end1 of paired-end fastq
  • fq_end2 (File?): GCS path to end2 of paired-end fastq
  • gcs_out_root_dir (String?): GCS Bucket into which to finalize outputs. If no bucket is given, outputs will not be finalized and instead will remain in their native execution location.
  • input_bai (File?): GCS path to bai index for unmapped bam
  • input_bam (File?): GCS path to unmapped bam
  • t_004_RevertSam.runtime_attr_override (RuntimeAttr?)
  • t_005_Bam2Fastq.bam_index (File?)
  • t_005_Bam2Fastq.reference_dict (File?)
  • t_005_Bam2Fastq.reference_fasta (File?)
  • t_005_Bam2Fastq.reference_fasta_index (File?)
  • t_005_Bam2Fastq.runtime_attr_override (RuntimeAttr?)
  • t_006_GetRawReadGroup.runtime_attr_override (RuntimeAttr?)
  • t_007_AlignReads.runtime_attr_override (RuntimeAttr?)
  • t_008_ExtractDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_009_ExtractContaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_010_SortDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_011_SortContaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_012_CreateFastqFromDecontaminatedReads.bam_index (File?)
  • t_012_CreateFastqFromDecontaminatedReads.reference_dict (File?)
  • t_012_CreateFastqFromDecontaminatedReads.reference_fasta (File?)
  • t_012_CreateFastqFromDecontaminatedReads.reference_fasta_index (File?)
  • t_012_CreateFastqFromDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_013_FinalizeContaminatedBam.name (String?)
  • t_013_FinalizeContaminatedBam.runtime_attr_override (RuntimeAttr?)
  • t_014_FinalizeContaminatedBamIndex.name (String?)
  • t_014_FinalizeContaminatedBamIndex.runtime_attr_override (RuntimeAttr?)
  • t_015_FinalizeDecontaminatedFq1.name (String?)
  • t_015_FinalizeDecontaminatedFq1.runtime_attr_override (RuntimeAttr?)
  • t_016_FinalizeDecontaminatedFq2.name (String?)
  • t_016_FinalizeDecontaminatedFq2.runtime_attr_override (RuntimeAttr?)
  • t_017_FinalizeDecontaminatedUnpaired.name (String?)
  • t_017_FinalizeDecontaminatedUnpaired.runtime_attr_override (RuntimeAttr?)

Defaults

  • DEBUG_MODE (Boolean, default=false): [default valued] enables debugging tasks / subworkflows (default: false)
  • platform (String, default="illumina"): [default valued] the value to place in the BAM read group's PL (platform) field (default: illumina)
  • t_001_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • t_007_AlignReads.skip_sort (Boolean, default=false)
  • t_009_ExtractContaminatedReads.extra_args (String, default="")

Outputs

  • contaminated_bam (File)
  • contaminated_bam_index (File)
  • decontaminated_fq1 (File)
  • decontaminated_fq2 (File)
  • decontaminated_unpaired (File)

Dot Diagram

RemoveSingleOrganismContamination