PBMASIsoSeqQuantify

PBMASIsoSeqQuantify

description
A workflow that performs processing of MAS-ISO-seq data on a single sample from one or more flow cells. The workflow merges multiple samples into a single BAM prior to processing.

Quantifies RNA isoform expression from given extracted, aligned, UMI- and CBC-annotated MAS-ISO-seq reads.

Inputs

Required

  • aligned_ccs_bais (Array[File], required): GCS path to aligned MAS-ISO-seq CCS BAM file indices
  • aligned_ccs_bams (Array[File], required): GCS path to aligned MAS-ISO-seq CCS BAM files
  • gcs_out_root_dir (String, required): GCS bucket to store the corrected/uncorrected reads, variants, and metrics files
  • participant_name (String, required): name of the participant from whom these samples were obtained
  • ref_gtf (File, required): GTF file to use for quantification
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • interval_overlap_name (String?): [optional] The name of the annotation to add to the final anndata object for the column containing the overlap flag for transcripts that overlap intervals in the given intervals_of_interest file.
  • intervals_of_interest (File?): [optional] An interval list file containing intervals to mark in the final anndata object as overlapping the transcripts.
  • t_02_MergeAllReads.runtime_attr_override (RuntimeAttr?)
  • t_03_AlignmentFilterArrayElements.runtime_attr_override (RuntimeAttr?)
  • t_03_RestoreSingleCellBamTagsForMasIsoSeqV0.runtime_attr_override (RuntimeAttr?)
  • t_04_IndexFilteredReads.runtime_attr_override (RuntimeAttr?)
  • t_05_Stringtie2_Quantify.runtime_attr_override (RuntimeAttr?)
  • t_06_Stringtie2_ExtractTranscriptSequences.runtime_attr_override (RuntimeAttr?)
  • t_07_Stringtie2_CompareTranscriptomes.runtime_attr_override (RuntimeAttr?)
  • t_08_GffCompareStringtie2toGencode.runtime_attr_override (RuntimeAttr?)
  • t_09_GffCompareGencodetoStringtie2.runtime_attr_override (RuntimeAttr?)
  • t_10_RestoreOriginalReadNames.runtime_attr_override (RuntimeAttr?)
  • t_11_MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • t_12_SubsetBam.runtime_attr_override (RuntimeAttr?)
  • t_13_ConvertSplicedBamToGff.runtime_attr_override (RuntimeAttr?)
  • t_14_GffCompareStringtie2toMasSeqReads.runtime_attr_override (RuntimeAttr?)
  • t_15_GffCompareGencodetoMasSeqReads.runtime_attr_override (RuntimeAttr?)
  • t_16_QuantifyGffComparison.runtime_attr_override (RuntimeAttr?)
  • t_17_CombineEqClassFiles.runtime_attr_override (RuntimeAttr?)
  • t_18_CopyEqClassInfoToTag.runtime_attr_override (RuntimeAttr?)
  • t_19_CorrectUmisWithSetCover.runtime_attr_override (RuntimeAttr?)
  • t_20_CreateCCSCountMatrixFromAnnotatedBam.runtime_attr_override (RuntimeAttr?)
  • t_22_FinalizeBam.runtime_attr_override (RuntimeAttr?)
  • t_23_FinalizeBai.runtime_attr_override (RuntimeAttr?)
  • t_24_FinalizeEqClassesGeneDefs.name (String?)
  • t_24_FinalizeEqClassesGeneDefs.runtime_attr_override (RuntimeAttr?)
  • t_25_FinalizeEqClassesGeneAssignments.name (String?)
  • t_25_FinalizeEqClassesGeneAssignments.runtime_attr_override (RuntimeAttr?)
  • t_26_FinalizeEqClassesTranscriptDefs.name (String?)
  • t_26_FinalizeEqClassesTranscriptDefs.runtime_attr_override (RuntimeAttr?)
  • t_27_FinalizeEqClassesTranscriptAssignments.name (String?)
  • t_27_FinalizeEqClassesTranscriptAssignments.runtime_attr_override (RuntimeAttr?)
  • t_28_FinalizeCCSCountMatrix.name (String?)
  • t_28_FinalizeCCSCountMatrix.runtime_attr_override (RuntimeAttr?)
  • t_29_FinalizeCCSCountMatrixAnnData.name (String?)
  • t_29_FinalizeCCSCountMatrixAnnData.runtime_attr_override (RuntimeAttr?)
  • t_30_FinalizeCCSRawQuantPickles.runtime_attr_override (RuntimeAttr?)
  • t_31_FinalizeRefAndSt2Comparisons.runtime_attr_override (RuntimeAttr?)
  • t_32_FinalizeTxAndGeneAssignmentsByContig.runtime_attr_override (RuntimeAttr?)
  • t_33_FinalizeIntermediateAnnotatedArrayElements.runtime_attr_override (RuntimeAttr?)
  • t_34_FinalizeAnnotatedArrayElements.runtime_attr_override (RuntimeAttr?)
  • t_35_FinalizeDiscoveredTranscriptome.runtime_attr_override (RuntimeAttr?)

Defaults

  • DEBUG_MODE (Boolean, default=false): [default valued] enables debugging tasks / subworkflows (default: false)
  • t_01_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • t_03_AlignmentFilterArrayElements.maxEndClipping (Int, default=1000)
  • t_03_AlignmentFilterArrayElements.maxReadLength (Int, default=15000)
  • t_12_SubsetBam.prefix (String, default="subset")
  • t_18_CopyEqClassInfoToTag.eq_class_tag (String, default="eq")
  • t_18_CopyEqClassInfoToTag.gene_tag (String, default="XG")
  • t_19_CorrectUmisWithSetCover.is_extracted (Boolean, default=true)
  • t_21_CreateCCSCountMatrixAnndataFromEqClasses.force_anndata_gencode_overwrite (Boolean, default=false)

Outputs

  • merged_input_bam (File)
  • merged_input_bai (File)
  • gene_eq_class_defs (File)
  • gene_eq_class_assignments (File)
  • transcript_eq_class_defs (File)
  • transcript_eq_class_assignments (File)
  • raw_count_matrix (File)
  • count_matrix_anndata (File)
  • raw_quant_pickle_gcs_dir (String)
  • ref_stringtie2_comparison_gcs_dir (String)
  • tx_gene_assignments_gcs_dir (Array[String])
  • intermediate_read_gcs_dir (String)
  • annotated_array_element_gcs_dir (String)
  • discovered_transcriptome_gcs_dir (String)

Dot Diagram

PBMASIsoSeqQuantify