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Made MarkDuplicates optional to enable Amplicon data processing.
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@jonn-smith
jonn-smith committed Jan 27, 2025
1 parent 2cf788b commit f7c708d
Showing 1 changed file with 41 additions and 25 deletions.
66 changes: 41 additions & 25 deletions wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@ workflow SRFlowcell {

perform_BQSR: "If true, will perform Base Quality Score Recalibration. If false will not recalibrate base qualities."

perform_mark_duplicates: "If true, will run MarkDuplicates on the raw reads from the sequencer."

DEBUG_MODE: "If true, will add extra logging and extra debugging outputs."

platform: "Platform on which the sample for the given bam file was sequenced."
Expand Down Expand Up @@ -62,6 +64,8 @@ workflow SRFlowcell {

Boolean perform_BQSR = true

Boolean perform_mark_duplicates = true

Boolean DEBUG_MODE = false

String platform = "illumina"
Expand Down Expand Up @@ -162,18 +166,21 @@ workflow SRFlowcell {

File merged_bam = select_first([t_007_MergeBamAlignment.bam, t_006_AlignReads.bam])

# Mark Duplicates
call SRUTIL.MarkDuplicates as t_008_MarkDuplicates {
input:
input_bam = merged_bam,
prefix = SM + ".aligned.merged.markDuplicates"
if (perform_mark_duplicates) {
# Mark Duplicates
call SRUTIL.MarkDuplicates as t_008_MarkDuplicates {
input:
input_bam = merged_bam,
prefix = SM + ".aligned.merged.markDuplicates"
}
}
File pre_bqsr_bam = select_first([t_008_MarkDuplicates.bam, merged_bam])

# Sort Duplicate Marked Bam:
call Utils.SortSam as t_009_SortAlignedDuplicateMarkedBam {
call Utils.SortSam as t_009_SortBam {
input:
input_bam = t_008_MarkDuplicates.bam,
prefix = SM + ".aligned.merged.markDuplicates.sorted"
input_bam = pre_bqsr_bam,
prefix = basename(pre_bqsr_bam, ".bam") + ".sorted"
}

# TODO: Add Fingerprinting?
Expand All @@ -182,8 +189,8 @@ workflow SRFlowcell {
# Recalibrate Base Scores:
call SRUTIL.BaseRecalibrator as t_010_BaseRecalibrator {
input:
input_bam = t_009_SortAlignedDuplicateMarkedBam.output_bam,
input_bam_index = t_009_SortAlignedDuplicateMarkedBam.output_bam_index,
input_bam = t_009_SortBam.output_bam,
input_bam_index = t_009_SortBam.output_bam_index,

ref_fasta = ref_map["fasta"],
ref_fasta_index = ref_map["fai"],
Expand All @@ -197,8 +204,8 @@ workflow SRFlowcell {

call SRUTIL.ApplyBQSR as t_011_ApplyBQSR {
input:
input_bam = t_009_SortAlignedDuplicateMarkedBam.output_bam,
input_bam_index = t_009_SortAlignedDuplicateMarkedBam.output_bam,
input_bam = t_009_SortBam.output_bam,
input_bam_index = t_009_SortBam.output_bam,

ref_fasta = ref_map["fasta"],
ref_fasta_index = ref_map["fai"],
Expand All @@ -210,8 +217,8 @@ workflow SRFlowcell {
}
}

File final_bam = select_first([t_011_ApplyBQSR.recalibrated_bam, t_009_SortAlignedDuplicateMarkedBam.output_bam])
File final_bai = select_first([t_011_ApplyBQSR.recalibrated_bai, t_009_SortAlignedDuplicateMarkedBam.output_bam_index])
File final_bam = select_first([t_011_ApplyBQSR.recalibrated_bam, t_009_SortBam.output_bam])
File final_bai = select_first([t_011_ApplyBQSR.recalibrated_bai, t_009_SortBam.output_bam_index])

#############################################
# __ __ _ _
Expand Down Expand Up @@ -336,9 +343,9 @@ workflow SRFlowcell {
[
t_006_AlignReads.bam,
merged_bam,
t_008_MarkDuplicates.bam,
t_009_SortAlignedDuplicateMarkedBam.output_bam,
t_009_SortAlignedDuplicateMarkedBam.output_bam_index,
pre_bqsr_bam,
t_009_SortBam.output_bam,
t_009_SortBam.output_bam_index,
],
keyfile = keyfile
}
Expand All @@ -363,7 +370,6 @@ workflow SRFlowcell {
outdir = metrics_dir,
files =
[
t_008_MarkDuplicates.metrics,
t_012_SamStats.sam_stats,
t_015_ComputeBamStats.results_file,
t_016_ComputeBamStatsQ5.results_file,
Expand All @@ -375,17 +381,27 @@ workflow SRFlowcell {
keyfile = keyfile
}

# Finalize BQSR Metrics if it was run:
if (perform_mark_duplicates) {
call FF.FinalizeToDir as t_028_FinalizeMarkDuplicatesMetrics {
input:
outdir = metrics_dir,
files = select_all([t_008_MarkDuplicates.metrics]),
keyfile = keyfile
}
}

# Finalize BQSR Metrics if it was run:
if (perform_BQSR) {
call FF.FinalizeToDir as t_028_FinalizeBQSRMetrics {
call FF.FinalizeToDir as t_029_FinalizeBQSRMetrics {
input:
outdir = metrics_dir,
files = select_all([t_010_BaseRecalibrator.recalibration_report]),
keyfile = keyfile
}
}

call FF.FinalizeToFile as t_029_FinalizeFastQCReport {
call FF.FinalizeToFile as t_030_FinalizeFastQCReport {
input:
outdir = metrics_dir,
file = t_013_FastQC.report
Expand All @@ -400,14 +416,14 @@ workflow SRFlowcell {
File fqboup = unaligned_reads_dir + "/" + basename(select_first([t_005_DecontaminateSample.decontaminated_unpaired, t_003_Bam2Fastq.fq_unpaired]))
}

call FF.FinalizeToFile as t_030_FinalizeCallableLociSummary {
call FF.FinalizeToFile as t_031_FinalizeCallableLociSummary {
input:
outdir = metrics_dir,
file = t_022_CallableLoci.callable_loci_summary,
keyfile = keyfile
}

call FF.FinalizeToFile as t_031_FinalizeCallableLociBed {
call FF.FinalizeToFile as t_032_FinalizeCallableLociBed {
input:
outdir = metrics_dir,
file = t_022_CallableLoci.callable_loci_bed,
Expand Down Expand Up @@ -481,10 +497,10 @@ workflow SRFlowcell {

Float average_identity = average_identity_value

File fastqc_report = select_first([t_029_FinalizeFastQCReport.gcs_path, t_013_FastQC.report])
File fastqc_report = select_first([t_030_FinalizeFastQCReport.gcs_path, t_013_FastQC.report])

File callable_loci_summary = select_first([t_030_FinalizeCallableLociSummary.gcs_path, t_022_CallableLoci.callable_loci_summary])
File callable_loci_bed = select_first([t_031_FinalizeCallableLociBed.gcs_path, t_022_CallableLoci.callable_loci_bed])
File callable_loci_summary = select_first([t_031_FinalizeCallableLociSummary.gcs_path, t_022_CallableLoci.callable_loci_summary])
File callable_loci_bed = select_first([t_032_FinalizeCallableLociBed.gcs_path, t_022_CallableLoci.callable_loci_bed])

String? qc_status = t_024_AssessQualityMetrics.qc_status
String? qc_message = t_024_AssessQualityMetrics.qc_message
Expand Down

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