SRFlowcell

SRFlowcell

author
Jonn Smith
description
This workflow preprocesses short read flowcell data in preparation for variant calling. This workflow contains the following steps: 1) Sam -> Fastq (if necessary), 2) Alignment to reference with bwa-mem2 (https://github.com/bwa-mem2/bwa-mem2), 3) Mark Duplicate reads, 4) Recalibrate base quality scores.

Inputs

Required

  • LB (String, required)
  • SM (String, required): Sample name for the given bam file.
  • dir_prefix (String, required): Directory prefix to use for finalized location.
  • ref_map_file (File, required): Reference map file for the primary reference sequence and auxillary file locations.

Optional

  • bai (File?): Index for bam. bam must be defined if this argument is. This argument and bam are mutually exclusive with fq_end1 and fq_end2
  • bam (File?): Bam file containing reads to align and process. bai must be defined if this argument is. This argument and bai are mutually exclusive with fq_end1 and fq_end2
  • contaminant_ref_map_file (File?): Reference map file for the contaminant reference sequence and auxillary file locations.
  • contaminant_ref_name (String?): Name for the contaminant reference.
  • coverage_bed_file (File?): BED file containing regions to calculate coverage metrics for.
  • fq_end1 (File?): FASTQ file containing end 1 of the short read data to process. fq_end2 must be defined if this argument is. This argument and fq_end2 are mutually exclusive with bam and bai
  • fq_end2 (File?): FASTQ file containing end 2 of the short read data to process. fq_end1 must be defined if this argument is. This argument and fq_end1 are mutually exclusive with bam and bai
  • 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.
  • t_002_RevertSam.runtime_attr_override (RuntimeAttr?)
  • t_003_Bam2Fastq.bam_index (File?)
  • t_003_Bam2Fastq.reference_dict (File?)
  • t_003_Bam2Fastq.reference_fasta (File?)
  • t_003_Bam2Fastq.reference_fasta_index (File?)
  • t_003_Bam2Fastq.runtime_attr_override (RuntimeAttr?)
  • t_004_GetRawReadGroup.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.input_bai (File?)
  • t_005_DecontaminateSample.input_bam (File?)
  • t_006_AlignReads.runtime_attr_override (RuntimeAttr?)
  • t_007_MergeBamAlignment.runtime_attr_override (RuntimeAttr?)
  • t_008_MarkDuplicates.read_name_regex (String?)
  • t_008_MarkDuplicates.runtime_attr_override (RuntimeAttr?)
  • t_008_MarkDuplicates.sorting_collection_size_ratio (Float?)
  • t_009_SortBam.runtime_attr_override (RuntimeAttr?)
  • t_010_BaseRecalibrator.runtime_attr_override (RuntimeAttr?)
  • t_011_ApplyBQSR.runtime_attr_override (RuntimeAttr?)
  • t_012_SamStats.runtime_attr_override (RuntimeAttr?)
  • t_013_FastQC.runtime_attr_override (RuntimeAttr?)
  • t_014_ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • t_015_ComputeBamStats.qual_threshold (Int?)
  • t_015_ComputeBamStats.runtime_attr_override (RuntimeAttr?)
  • t_016_ComputeBamStatsQ5.runtime_attr_override (RuntimeAttr?)
  • t_017_ComputeBamStatsQ10.runtime_attr_override (RuntimeAttr?)
  • t_018_ComputeBamStatsQ20.runtime_attr_override (RuntimeAttr?)
  • t_019_ComputeBamStatsQ30.runtime_attr_override (RuntimeAttr?)
  • t_020_ComputeBamStatsQ40.runtime_attr_override (RuntimeAttr?)
  • t_022_CallableLoci.runtime_attr_override (RuntimeAttr?)
  • t_022_FinalizeUnalignedFastqReads.runtime_attr_override (RuntimeAttr?)
  • t_023_FinalizeUnalignedReadsFromBam.runtime_attr_override (RuntimeAttr?)
  • t_023_MosDepthOverBed.runtime_attr_override (RuntimeAttr?)
  • t_024_AssessQualityMetrics.runtime_attr_override (RuntimeAttr?)
  • t_024_FinalizeAlignedReads.runtime_attr_override (RuntimeAttr?)
  • t_025_FinalizeAlignedBam.name (String?)
  • t_025_FinalizeAlignedBam.runtime_attr_override (RuntimeAttr?)
  • t_026_FinalizeAlignedBai.name (String?)
  • t_026_FinalizeAlignedBai.runtime_attr_override (RuntimeAttr?)
  • t_027_FinalizeMetrics.runtime_attr_override (RuntimeAttr?)
  • t_028_FinalizeMarkDuplicatesMetrics.runtime_attr_override (RuntimeAttr?)
  • t_029_FinalizeBQSRMetrics.runtime_attr_override (RuntimeAttr?)
  • t_030_FinalizeFastQCReport.keyfile (File?)
  • t_030_FinalizeFastQCReport.name (String?)
  • t_030_FinalizeFastQCReport.runtime_attr_override (RuntimeAttr?)
  • t_031_FinalizeCallableLociSummary.name (String?)
  • t_031_FinalizeCallableLociSummary.runtime_attr_override (RuntimeAttr?)
  • t_032_FinalizeCallableLociBed.name (String?)
  • t_032_FinalizeCallableLociBed.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_004_RevertSam.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_005_Bam2Fastq.bam_index (File?)
  • t_005_DecontaminateSample.t_005_Bam2Fastq.reference_dict (File?)
  • t_005_DecontaminateSample.t_005_Bam2Fastq.reference_fasta (File?)
  • t_005_DecontaminateSample.t_005_Bam2Fastq.reference_fasta_index (File?)
  • t_005_DecontaminateSample.t_005_Bam2Fastq.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_006_GetRawReadGroup.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_007_AlignReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_008_ExtractDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_009_ExtractContaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_010_SortDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_011_SortContaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_012_CreateFastqFromDecontaminatedReads.bam_index (File?)
  • t_005_DecontaminateSample.t_012_CreateFastqFromDecontaminatedReads.reference_dict (File?)
  • t_005_DecontaminateSample.t_012_CreateFastqFromDecontaminatedReads.reference_fasta (File?)
  • t_005_DecontaminateSample.t_012_CreateFastqFromDecontaminatedReads.reference_fasta_index (File?)
  • t_005_DecontaminateSample.t_012_CreateFastqFromDecontaminatedReads.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_013_FinalizeContaminatedBam.name (String?)
  • t_005_DecontaminateSample.t_013_FinalizeContaminatedBam.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_014_FinalizeContaminatedBamIndex.name (String?)
  • t_005_DecontaminateSample.t_014_FinalizeContaminatedBamIndex.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_015_FinalizeDecontaminatedFq1.name (String?)
  • t_005_DecontaminateSample.t_015_FinalizeDecontaminatedFq1.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_016_FinalizeDecontaminatedFq2.name (String?)
  • t_005_DecontaminateSample.t_016_FinalizeDecontaminatedFq2.runtime_attr_override (RuntimeAttr?)
  • t_005_DecontaminateSample.t_017_FinalizeDecontaminatedUnpaired.name (String?)
  • t_005_DecontaminateSample.t_017_FinalizeDecontaminatedUnpaired.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.AlignedFlagStats.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.AlignedReadMetrics.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageFullDist.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageFullDist.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageGlobalDist.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageGlobalDist.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantized.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantized.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantizedCsi.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantizedCsi.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantizedDist.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageQuantizedDist.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageRegionDist.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageRegionDist.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageRegions.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageRegions.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFCoverageRegionsCsi.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFCoverageRegionsCsi.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFDepthSummaries.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFDepthSummaries.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.FFYieldAligned.keyfile (File?)
  • t_021_PerFlowcellMetrics.FFYieldAligned.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.MosDepth.runtime_attr_override (RuntimeAttr?)
  • t_021_PerFlowcellMetrics.MosDepth.window_size (Int?)
  • t_021_PerFlowcellMetrics.SummarizeDepth.runtime_attr_override (RuntimeAttr?)

Defaults

  • DEBUG_MODE (Boolean, default=false): If true, will add extra logging and extra debugging outputs.
  • perform_BQSR (Boolean, default=true): If true, will perform Base Quality Score Recalibration. If false will not recalibrate base qualities.
  • perform_mark_duplicates (Boolean, default=true): If true, will run MarkDuplicates on the raw reads from the sequencer.
  • platform (String, default="illumina"): Platform on which the sample for the given bam file was sequenced.
  • t_001_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • t_005_DecontaminateSample.DEBUG_MODE (Boolean, default=false): If true, will add extra logging and extra debugging outputs.
  • t_011_ApplyBQSR.bin_base_qualities (Boolean, default=true)
  • t_011_ApplyBQSR.emit_original_quals (Boolean, default=true)
  • t_013_FastQC.num_cpus (Int, default=4)
  • t_022_CallableLoci.min_base_quality (Int, default=20)
  • t_022_CallableLoci.min_mapping_quality (Int, default=10)
  • t_024_AssessQualityMetrics.min_callable_fraction (Float, default=0.5)
  • t_024_AssessQualityMetrics.min_coverage (Float, default=5)
  • t_024_AssessQualityMetrics.min_coverage_threshold_regions (Float, default=0.2)
  • t_005_DecontaminateSample.t_001_WdlExecutionStartTimestamp.date_format (String, default="%Y%m%d_%H%M%S_%N")
  • t_005_DecontaminateSample.t_007_AlignReads.skip_sort (Boolean, default=false)
  • t_005_DecontaminateSample.t_009_ExtractContaminatedReads.extra_args (String, default="")

Outputs

  • fq1 (File)
  • fq2 (File)
  • fq_unpaired (File?)
  • unaligned_bam (File?)
  • unaligned_bai (File?)
  • aligned_bam (File)
  • aligned_bai (File)
  • contaminated_bam (File?)
  • contaminated_bam_index (File?)
  • num_reads (Float)
  • num_bases (Float)
  • raw_est_fold_cov (Float)
  • read_length (Float)
  • read_qual_mean (Float)
  • read_qual_median (Float)
  • num_reads_Q5 (Float)
  • num_reads_Q10 (Float)
  • num_reads_Q20 (Float)
  • num_reads_Q30 (Float)
  • num_reads_Q40 (Float)
  • aligned_num_reads (Float)
  • aligned_num_bases (Float)
  • aligned_frac_bases (Float)
  • aligned_est_fold_cov (Float)
  • aligned_read_length (Float)
  • insert_size_average (Float)
  • insert_size_standard_deviation (Float)
  • pct_properly_paired_reads (Float)
  • average_identity (Float)
  • fastqc_report (File)
  • callable_loci_summary (File)
  • callable_loci_bed (File)
  • qc_status (String?)
  • qc_message (String?)

Dot Diagram

SRFlowcell