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SHuang-BroadSHuang-Broad
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DEPRECATION
 * AlignAndCheckFingerprintCCS.wdl * CollectPacBioAlignedMetrics.wdl * CollectSMRTCellUnalignedMetrics.wdl
1 parent 5bf0b2f commit 0d61935

5 files changed

Lines changed: 42 additions & 17 deletions

wdl/tasks/Alignment/AlignAndCheckFingerprintCCS.wdl renamed to wdl/deprecated/AlignAndCheckFingerprintCCS.wdl

Lines changed: 32 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,13 @@
11
version 1.0
22

3-
import "../QC/FPCheckAoU.wdl" as FPCheck
4-
import "../QC/CollectPacBioAlignedMetrics.wdl" as AlnMetrics
5-
import "../Utility/PBUtils.wdl" as PB
6-
import "../Utility/Utils.wdl"
7-
import "../Utility/GeneralUtils.wdl"
3+
import "../tasks/Utility/PBUtils.wdl" as PB
4+
import "../tasks/Utility/Utils.wdl"
5+
import "../tasks/Utility/GeneralUtils.wdl"
6+
import "../tasks/Utility/BAMutils.wdl" as BU
7+
8+
import "CollectPacBioAlignedMetrics.wdl" as AlnMetrics
9+
import "../tasks/QC/AlignedMetrics.wdl" as GeAlnMetrics
10+
import "../tasks/QC/FPCheckAoU.wdl" as FPCheck
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workflow AlignAndCheckFingerprintCCS {
1013
meta {
@@ -13,10 +16,10 @@ workflow AlignAndCheckFingerprintCCS {
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}
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input {
16-
File uBAM
17-
File uPBI
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File uBAM
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File? uPBI
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String bam_sample_name
19-
String library
22+
String? library
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Boolean turn_off_fingperprint_check
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String fp_store
@@ -40,6 +43,10 @@ workflow AlignAndCheckFingerprintCCS {
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4144
Map[String, String] ref_map = read_map(ref_map_file)
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46+
call BU.GetReadGroupInfo as RG {input: bam = uBAM, keys = ['SM', 'LB', 'PU']}
47+
String LB = select_first([library, RG.read_group_info['LB']])
48+
String movie_name = RG.read_group_info['PU']
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###################################################################################
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if (ceil(size(uBAM, "GB")) > 50) {# shard & align, but practically never true
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@@ -52,10 +59,13 @@ workflow AlignAndCheckFingerprintCCS {
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call Utils.ComputeAllowedLocalSSD as Guess {input: intended_gb = 3*ceil(size(uBAM, "GB") + size(uPBI, "GB"))}
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call Utils.RandomZoneSpewer as arbitrary {input: num_of_zones = 3}
62+
if (! defined(uPBI) ) {
63+
call PB.PBIndex as PBIndex {input: bam = uBAM}
64+
}
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call PB.ShardLongReads {
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input:
58-
unaligned_bam = uBAM, unaligned_pbi = uPBI,
68+
unaligned_bam = uBAM, unaligned_pbi = select_first([uPBI, PBIndex.pbi]),
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num_shards = 50, num_ssds = Guess.numb_of_local_ssd, zones = arbitrary.zones
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}
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@@ -109,24 +119,37 @@ workflow AlignAndCheckFingerprintCCS {
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name = "alignment.metrics"
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}
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call BU.SamtoolsFlagStats { input: bam = aBAM, output_format = 'JSON' }
123+
call BU.ParseFlagStatsJson { input: sam_flag_stats_json = SamtoolsFlagStats.flag_stats }
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112125
if (!turn_off_fingperprint_check){
113126
call FPCheck.FPCheckAoU {
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input:
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aligned_bam = aBAM,
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aligned_bai = aBAI,
130+
tech = 'Sequel', # making assumption that data to process here are all Sequel data (no critial impact though)
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fp_store = fp_store,
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sample_id_at_store = sample_id_at_store,
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ref_specific_haplotype_map = ref_map['haplotype_map']
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}
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call GeneralUtils.TarGZFiles as saveFPRes {input: files = [FPCheckAoU.fingerprint_summary, FPCheckAoU.fingerprint_details], name = 'fingerprint_check.summary_and_details'}
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}
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138+
call GeAlnMetrics.MosDepthWGS { input: bam = aBAM, bai = aBAI }
139+
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output {
125141
File aligned_bam = aBAM
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File aligned_bai = aBAI
127143
File aligned_pbi = IndexAlignedReads.pbi
128144

145+
String movie = movie_name
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147+
Float wgs_cov = MosDepthWGS.wgs_cov
148+
File coverage_per_chr = MosDepthWGS.summary_txt
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129150
File alignment_metrics_tar_gz = saveAlnMetrics.you_got_it
151+
Map[String, Float] alignment_metrics = CollectPacBioAlignedMetrics.alignment_metrics
152+
Map[String, Float] sam_flag_stats = ParseFlagStatsJson.qc_pass_reads_SAM_flag_stats
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131154
Float? fp_lod_expected_sample = FPCheckAoU.lod_expected_sample
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String? fp_status = FPCheckAoU.FP_status

wdl/tasks/QC/CollectPacBioAlignedMetrics.wdl renamed to wdl/deprecated/CollectPacBioAlignedMetrics.wdl

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
version 1.0
22

3-
import "../Utility/PBUtils.wdl" as PB
4-
import "../Visualization/NanoPlot.wdl" as NP
3+
import "../tasks/Utility/PBUtils.wdl" as PB
4+
import "../tasks/Visualization/NanoPlot.wdl" as NP
55

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workflow CollectPacBioAlignedMetrics {
77

@@ -46,6 +46,7 @@ workflow CollectPacBioAlignedMetrics {
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output {
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File custom_aln_metrics_summary = CustomMetricsSummaryToFile.custom_aln_metrics_summary
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File nanoplot_stats = NanoPlotFromBam.stats
49+
Map[String, Float] alignment_metrics = NanoPlotFromBam.stats_map
4950
Array[File] nanoplot_pngs = NanoPlotFromBam.plots
5051
}
5152
}

wdl/tasks/QC/CollectSMRTCellUnalignedMetrics.wdl renamed to wdl/deprecated/CollectSMRTCellUnalignedMetrics.wdl

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
version 1.0
22

3-
import "../Utility/PBUtils.wdl" as PB
4-
import "../Utility/Utils.wdl"
3+
import "../tasks/Utility/PBUtils.wdl" as PB
4+
import "../tasks/Utility/Utils.wdl"
55

66
workflow CollectSMRTCellUnalignedMetrics {
77

‎wdl/deprecated/PostprocessCCSedDemultiplexedSMRTCell.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
version 1.0
22

3-
import "../tasks/Alignment/AlignAndCheckFingerprintCCS.wdl" as major
3+
import "AlignAndCheckFingerprintCCS.wdl" as major
44
import "../tasks/Utility/BAMutils.wdl"
55
import "../tasks/Utility/Utils.wdl"
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import "../tasks/Utility/GeneralUtils.wdl" as GU

‎wdl/deprecated/PreprocessBarcodedCCSedSMRTCell.wdl‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,10 @@ version 1.0
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import "tasks/CCSLima.wdl"
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import "tasks/SMRTtools.wdl"
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import "../tasks/QC/CollectSMRTCellUnalignedMetrics.wdl" as uBAMCustomMetrics
6-
import "../tasks/Utility//PBUtils.wdl" as PB
7-
import "../tasks/Utility//Finalize.wdl" as FF
5+
import "CollectSMRTCellUnalignedMetrics.wdl" as uBAMCustomMetrics
6+
7+
import "../tasks/Utility/PBUtils.wdl" as PB
8+
import "../tasks/Utility/Finalize.wdl" as FF
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import "../tasks/Utility/Utils.wdl"
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import "../tasks/Utility/GeneralUtils.wdl" as GU
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