PBFlowcell

PBFlowcell

description
The workflow performs the alignment of an SMRT cell's worth of data to a reference. For genomic sequencing data, the workflow also optionally performs CCS correction if the data is from a CCS library but did not get corrected on-instrument. For MAS-seq transcriptome data, this workflow will determine the most likely MAS-seq model, then it will use that model to annotate, segment, and filter the CCS reads. These CCS reads will then be aligned to the reference in trascriptome alignemnt mode. Note: Currently the MAS-seq workflow separates CLR reads, but does not process them.

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
  • bam (File, required): GCS path to raw subread bam
  • dir_prefix (String, required): directory prefix for output files
  • experiment_type (String, required): type of experiment run (CLR, CCS, ISOSEQ, MASSEQ)
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • pbi (File, required): GCS path to pbi index for raw subread bam
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • ccs_report_txt (File?): GCS path to CCS report txt, required if on-instrument corrected, otherwise CCS is run in this workflow for CCS libraries
  • mas_seq_model (String?): Longbow model to use for MAS-seq data.
  • num_shards (Int?): number of shards into which fastq files should be batched
  • AlignReads.runtime_attr_override (RuntimeAttr?)
  • BamToFastq.runtime_attr_override (RuntimeAttr?)
  • CCS.runtime_attr_override (RuntimeAttr?)
  • ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • ExtractCcsReads.runtime_attr_override (RuntimeAttr?)
  • ExtractClrReads.runtime_attr_override (RuntimeAttr?)
  • ExtractHifiReads.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBai.name (String?)
  • FinalizeAlignedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedBam.name (String?)
  • FinalizeAlignedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeAlignedPbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeCCSReport.name (String?)
  • FinalizeCCSReport.runtime_attr_override (RuntimeAttr?)
  • FinalizeCCSUnalignedBai.name (String?)
  • FinalizeCCSUnalignedBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeCCSUnalignedBam.name (String?)
  • FinalizeCCSUnalignedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeCCSUnalignedPbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeFastq.runtime_attr_override (RuntimeAttr?)
  • FinalizeFilteredCCSStatsPNGs.runtime_attr_override (RuntimeAttr?)
  • FinalizeFilteredCCSStatsSVGs.runtime_attr_override (RuntimeAttr?)
  • FinalizeFilteredCCSStatsSummary.name (String?)
  • FinalizeFilteredCCSStatsSummary.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowAnnotatedBam.name (String?)
  • FinalizeLongbowAnnotatedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowCorrectLog.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowCorrectedBam.name (String?)
  • FinalizeLongbowCorrectedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowExtractedBam.name (String?)
  • FinalizeLongbowExtractedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowFilterFailedBam.name (String?)
  • FinalizeLongbowFilterFailedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowFilteredBam.name (String?)
  • FinalizeLongbowFilteredBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowIntermediateBamIndices.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowIntermediateSingleCellBamIndices.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowSegmentedBam.name (String?)
  • FinalizeLongbowSegmentedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowUmiAdjustmentLog.runtime_attr_override (RuntimeAttr?)
  • FinalizeLongbowUncorrectedBam.name (String?)
  • FinalizeLongbowUncorrectedBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeMasSeqLongbowCorrectStats.runtime_attr_override (RuntimeAttr?)
  • FinalizeMasSeqUnprocessedCLRReads.name (String?)
  • FinalizeMasSeqUnprocessedCLRReads.runtime_attr_override (RuntimeAttr?)
  • FinalizeMasSeqUnprocessedCLRReadsBai.name (String?)
  • FinalizeMasSeqUnprocessedCLRReadsBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeOverallCCSStatsPNGs.runtime_attr_override (RuntimeAttr?)
  • FinalizeOverallCCSStatsSVGs.runtime_attr_override (RuntimeAttr?)
  • FinalizeOverallCCSStatsSummary.name (String?)
  • FinalizeOverallCCSStatsSummary.runtime_attr_override (RuntimeAttr?)
  • FixMasSeqCcsReadTagsPostAlignment.runtime_attr_override (RuntimeAttr?)
  • GetRawReadGroup.runtime_attr_override (RuntimeAttr?)
  • GetRunInfo.runtime_attr_override (RuntimeAttr?)
  • IndexAlignedReads.runtime_attr_override (RuntimeAttr?)
  • IndexCCSUnalignedReads.runtime_attr_override (RuntimeAttr?)
  • LongbowFilteredCCSStats.runtime_attr_override (RuntimeAttr?)
  • LongbowOverallCCSStats.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.barcode_allow_list (File?)
  • LongbowProcessCCS.barcode_tag (String?)
  • LongbowProcessCCS.corrected_tag (String?)
  • Longbow_Peek.runtime_attr_override (RuntimeAttr?)
  • MasseqCCSBamToFastq.runtime_attr_override (RuntimeAttr?)
  • MergeAlignedReads.runtime_attr_override (RuntimeAttr?)
  • MergeAllFastqs.runtime_attr_override (RuntimeAttr?)
  • MergeCCSReports.runtime_attr_override (RuntimeAttr?)
  • MergeCCSUnalignedReads.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowAnnotatedCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowCorrectedCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowExtractedCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowFilterFailedCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowFilteredCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowSegmentedCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeLongbowUncorrectableCCSBams.runtime_attr_override (RuntimeAttr?)
  • MergeMASSeqCLRReads.runtime_attr_override (RuntimeAttr?)
  • NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • RenameSingleCellBamTagsForMasIsoSeqV0.runtime_attr_override (RuntimeAttr?)
  • ShardLongReads.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ10PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ12PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ15PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ5PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeAlignedQ7PBI.runtime_attr_override (RuntimeAttr?)
  • SummarizeCCSReport.runtime_attr_override (RuntimeAttr?)
  • ValidateShard.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.AggregateCorrectLogStats.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.Extract.bam_pbi (File?)
  • LongbowProcessCCS.Extract.leading_adapter (String?)
  • LongbowProcessCCS.Extract.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.Extract.start_offset (Int?)
  • LongbowProcessCCS.Extract.trailing_adapter (String?)
  • LongbowProcessCCS.t_01_Peek.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_02_Annotate.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_03_Filter.bam_pbi (File?)
  • LongbowProcessCCS.t_03_Filter.model (String?)
  • LongbowProcessCCS.t_03_Filter.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_04_Segment.model (String?)
  • LongbowProcessCCS.t_04_Segment.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_05_RemoveMasSeqTruncatedReads.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_07_PadUMI.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_08_PadCBC.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_09_Correct.barcode_freq_list (File?)
  • LongbowProcessCCS.t_09_Correct.runtime_attr_override (RuntimeAttr?)
  • LongbowProcessCCS.t_10_AdjustUmiSequenceWithAdapterAlignment.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.AlignedFlagStats.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.AlignedReadMetrics.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageFullDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageFullDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageGlobalDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageGlobalDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantized.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantized.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantizedCsi.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantizedCsi.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageQuantizedDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageQuantizedDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegionDist.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegionDist.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegions.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegions.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFCoverageRegionsCsi.keyfile (File?)
  • PerFlowcellMetrics.FFCoverageRegionsCsi.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFDepthSummaries.keyfile (File?)
  • PerFlowcellMetrics.FFDepthSummaries.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.FFYieldAligned.keyfile (File?)
  • PerFlowcellMetrics.FFYieldAligned.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MosDepth.runtime_attr_override (RuntimeAttr?)
  • PerFlowcellMetrics.MosDepth.window_size (Int?)
  • PerFlowcellMetrics.SummarizeDepth.runtime_attr_override (RuntimeAttr?)

Defaults

  • DEBUG_MODE (Boolean, default=false): [default valued] enables debugging tasks / subworkflows (default: false)
  • drop_per_base_N_pulse_tags (Boolean, default=true)
  • validate_shards (Boolean, default=false)
  • AlignMasSeqCCSReads.prefix (String, default="out")
  • AlignReads.prefix (String, default="out")
  • CCS.all (Boolean, default=true)
  • CCS.by_strand (Boolean, default=false)
  • CCS.kinetics (Boolean, default=false)
  • ExtractHifiReads.prefix (String, default="hifi")
  • LongbowProcessCCS.same_barcode_per_read (Boolean, default=false)
  • LongbowProcessCCS.shard_width (Int, default=25)
  • MergeAllFastqs.prefix (String, default="merged")
  • ShardLongReads.num_threads (Int, default=8)
  • ShardLongReads.prefix (String, default="shard")
  • SummarizeSubreadsPBI.qual_threshold (Int, default=0)
  • WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • LongbowProcessCCS.Extract.base_padding (Int, default=2)
  • LongbowProcessCCS.Extract.num_cpus (Int, default=2)
  • LongbowProcessCCS.t_01_Peek.n (Int, default=100)
  • LongbowProcessCCS.t_02_Annotate.num_cpus (Int, default=8)
  • LongbowProcessCCS.t_03_Filter.num_cpus (Int, default=2)
  • LongbowProcessCCS.t_04_Segment.num_cpus (Int, default=2)
  • LongbowProcessCCS.t_07_PadUMI.padding (Int, default=2)
  • LongbowProcessCCS.t_08_PadCBC.padding (Int, default=2)
  • LongbowProcessCCS.t_09_Correct.ccs_lev_dist_threshold (Int, default=2)
  • LongbowProcessCCS.t_09_Correct.clr_lev_dist_threshold (Int, default=2)
  • LongbowProcessCCS.t_10_AdjustUmiSequenceWithAdapterAlignment.existing_umi_tag (String, default="ZU")
  • LongbowProcessCCS.t_10_AdjustUmiSequenceWithAdapterAlignment.new_umi_tag (String, default="JX")

Outputs

  • ccs_report (File?)
  • ccs_zmws_input (Float?)
  • ccs_zmws_pass_filters (Float?)
  • ccs_zmws_fail_filters (Float?)
  • ccs_zmws_shortcut_filters (Float?)
  • ccs_zmws_pass_filters_pct (Float?)
  • ccs_zmws_fail_filters_pct (Float?)
  • ccs_zmws_shortcut_filters_pct (Float?)
  • polymerase_read_length_mean (Float)
  • polymerase_read_length_N50 (Float)
  • subread_read_length_mean (Float)
  • subread_read_length_N50 (Float)
  • fq (File?)
  • ccs_bam (File?)
  • ccs_pbi (File?)
  • aligned_bam (File)
  • aligned_bai (File)
  • aligned_pbi (File)
  • num_reads (Float)
  • num_bases (Float)
  • raw_est_fold_cov (Float)
  • read_length_mean (Float)
  • read_length_median (Float)
  • read_length_stdev (Float)
  • read_length_N50 (Float)
  • read_qual_mean (Float)
  • read_qual_median (Float)
  • num_reads_Q5 (Float)
  • num_reads_Q7 (Float)
  • num_reads_Q10 (Float)
  • num_reads_Q12 (Float)
  • num_reads_Q15 (Float)
  • aligned_num_reads (Float)
  • aligned_num_bases (Float)
  • aligned_frac_bases (Float)
  • aligned_est_fold_cov (Float)
  • aligned_read_length_mean (Float)
  • aligned_read_length_median (Float)
  • aligned_read_length_stdev (Float)
  • aligned_read_length_N50 (Float)
  • average_identity (Float)
  • median_identity (Float)
  • library_type (String)
  • longbow_overall_ccs_stats_plots_png (String?)
  • longbow_overall_ccs_stats_plots_svg (String?)
  • longbow_overall_ccs_stats (File?)
  • longbow_filtered_ccs_stats_plots_png (String?)
  • longbow_filtered_ccs_stats_plots_svg (String?)
  • longbow_filtered_ccs_stats (File?)

Dot Diagram

PBFlowcell