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SHuang-BroadSHuang-Broad
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Two new workflows:
 handle (ref-indepedent, alignment) a single piece of on-instrument demultiplexed CCS bam
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‎.dockstore.yml‎

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- name: PBMASIsoSeqDemultiplex
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subclass: wdl
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primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqDemultiplex.wdl
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- name: ProcessOnInstrumentDemuxedChunkRefFree
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subclass: wdl
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primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunkRefFree.wdl
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- name: ProcessOnInstrumentDemuxedChunk
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subclass: wdl
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primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunk.wdl
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###################################################
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# TechAgnostic

‎wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunk.wdl‎

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version 1.0
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import "../../../tasks/Utility/PBUtils.wdl"
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import "../../../tasks/Utility/BAMutils.wdl" as BU
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import "../../../tasks/Utility/GeneralUtils.wdl" as GU
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import "../../../tasks/Utility/Finalize.wdl" as FF
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import "../../../tasks/Alignment/AlignAndCheckFingerprintCCS.wdl" as major
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import "../../../tasks/QC/AlignedMetrics.wdl"
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workflow ProcessOnInstrumentDemuxedChunk {
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meta {
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desciption: "!!! WARN: THIS IS PROJECT-CENTER SPECIFIC !!! Given an on-instrument demultiplexed hifi_reads.bam, perform alignment and QC check."
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}
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input {
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File uBAM
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File? uPBI
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String readgroup_id
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String bam_SM_field
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String fingerprint_store
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String sample_id_at_store
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Boolean turn_off_fingperprint_check = false
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File ref_map_file
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String gcs_out_root_dir
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}
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###################################################################################
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# prep work
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# where to store final results
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String workflow_name = "ProcessOnInstrumentDemuxedChunk"
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String outdir = sub(gcs_out_root_dir, "/$", "") + "/" + workflow_name
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###################################################################################
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call BU.GetReadGroupInfo as RG {input: bam = uBAM, keys = ['SM', 'LB', 'PU']}
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# major work
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call major.AlignAndCheckFingerprintCCS {
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input:
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uBAM = uBAM,
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uPBI = uPBI,
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bam_sample_name = bam_SM_field,
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library = RG.read_group_info['LB'],
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turn_off_fingperprint_check = turn_off_fingperprint_check,
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fp_store = fingerprint_store,
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sample_id_at_store = sample_id_at_store,
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ref_map_file = ref_map_file
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}
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###################################################################################
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# finalize
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String movie_name = RG.read_group_info['PU']
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String bc_specific_aln_out = outdir + '/alignments/' + readgroup_id
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String bc_specific_metric_out = outdir + "/metrics/" + readgroup_id
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call FF.FinalizeToFile as FinalizeAlignedBam { input: outdir = bc_specific_aln_out, file = AlignAndCheckFingerprintCCS.aligned_bam, name = readgroup_id + '.bam' }
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call FF.FinalizeToFile as FinalizeAlignedBai { input: outdir = bc_specific_aln_out, file = AlignAndCheckFingerprintCCS.aligned_bai, name = readgroup_id + '.bai' }
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call FF.FinalizeToFile as FinalizeAlignedPbi { input: outdir = bc_specific_aln_out, file = AlignAndCheckFingerprintCCS.aligned_pbi, name = readgroup_id + '.pbi' }
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call FF.FinalizeToFile as FinalizePerChrCov { input: outdir = bc_specific_metric_out, file = AlignAndCheckFingerprintCCS.coverage_per_chr }
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call FF.FinalizeToFile as FinalizeAlnMetrics { input: outdir = bc_specific_metric_out, file = AlignAndCheckFingerprintCCS.alignment_metrics_tar_gz }
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if (! turn_off_fingperprint_check) {
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call FF.FinalizeToFile as FinalizeFPDetails { input: outdir = bc_specific_metric_out, file = select_first([AlignAndCheckFingerprintCCS.fingerprint_detail_tar_gz]) }
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}
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###################################################################################
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call GU.GetTodayDate as today {}
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output {
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File aligned_bam = FinalizeAlignedBam.gcs_path
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File aligned_bai = FinalizeAlignedBai.gcs_path
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File aligned_pbi = FinalizeAlignedPbi.gcs_path
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Float wgs_cov = AlignAndCheckFingerprintCCS.wgs_cov
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File coverage_per_chr = FinalizePerChrCov.gcs_path
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Map[String, Float] alignment_metrics = AlignAndCheckFingerprintCCS.alignment_metrics
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File alignment_metrics_tar_gz = FinalizeAlnMetrics.gcs_path
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String movie = movie_name
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String? fingerprint_check_result = AlignAndCheckFingerprintCCS.fp_status
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Float? fingerprint_check_LOD = AlignAndCheckFingerprintCCS.fp_lod_expected_sample
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File? fingerprint_check_tar_gz = FinalizeFPDetails.gcs_path
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String last_processing_date = today.yyyy_mm_dd
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}
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}

‎wdl/pipelines/PacBio/Utility/ProcessOnInstrumentDemuxedChunkRefFree.wdl‎

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version 1.0
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import "../../../tasks/Visualization/NanoPlot.wdl"
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import "../../../tasks/Utility/Utils.wdl"
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import "../../../tasks/Utility/BAMutils.wdl" as BU
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import "../../../tasks/Utility/GeneralUtils.wdl" as GU
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import "../../../tasks/Utility/Finalize.wdl" as FF
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workflow ProcessOnInstrumentDemuxedChunkRefFree {
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meta {
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desciption: "!!! WARN: THIS IS PROJECT-CENTER SPECIFIC !!! Given an on-instrument demultiplexed hifi_reads.bam, perform ref-independent prep work."
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}
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input {
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File uBAM
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String readgroup_id
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String gcs_out_root_dir
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}
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###################################################################################
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# prep work
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# where to store final results
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String workflow_name = "ProcessOnInstrumentDemuxedChunkRefFree"
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String outdir = sub(gcs_out_root_dir, "/$", "") + "/" + workflow_name
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String outdir_ref_free = outdir + '/RefFree'
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###################################################################################
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# stats
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call NanoPlot.NanoPlotFromUBam {input: uBAM = uBAM}
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call BU.BamToFastq {input: bam = uBAM, prefix = "does_not_matter"}
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###################################################################################
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# finalize
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call BU.GetReadGroupInfo as RG {input: bam = uBAM, keys = ['PU']}
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String movie_name = RG.read_group_info['PU']
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String bc_specific_fastq_out = outdir_ref_free + '/' + readgroup_id
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call FF.FinalizeToFile as FinalizeFQ { input: outdir = bc_specific_fastq_out, file = BamToFastq.reads_fq, name = readgroup_id + '.hifi.fq.gz' }
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###################################################################################
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call GU.GetTodayDate as today {}
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output {
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String movie = movie_name
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File hifi_fq = FinalizeFQ.gcs_path
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Map[String, Float] hifi_stats = NanoPlotFromUBam.stats_map
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String last_processing_date = today.yyyy_mm_dd
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}
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}

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