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Make LocalizeReads Optional in GatherSampleEvidence #620

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merged 6 commits into from
Dec 14, 2023
Merged

Make LocalizeReads Optional in GatherSampleEvidence #620

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c1e4ca9
Added boolean variable to GatherSampleEvidence to indicate if Localiz…
kirtanav98 Nov 21, 2023
5bf1165
Removed redundant implementation of localized reads in GatherSampleEv…
kirtanav98 Nov 21, 2023
7728fe0
Updated GatherSampleEvidence rb.CramToBamReviseBase to use input cram…
kirtanav98 Nov 21, 2023
6366a79
Updated GatherSampleEvidence rb.CramToBamReviseBase to use input cram…
kirtanav98 Nov 27, 2023
aefb25e
Fixed the file to check for revise_bam, localize reads, and then uses…
kirtanav98 Nov 30, 2023
772b114
Changed location of variable and input to better flow with current wd…
kirtanav98 Dec 5, 2023
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18 changes: 13 additions & 5 deletions wdl/GatherSampleEvidence.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,10 @@ workflow GatherSampleEvidence {
# Only use if encountering errors (expensive!)
Boolean revise_base = false

# Localize reads parameters
# set to true on default, skips localize_reads if set to false
Boolean run_localize_reads = true

# Common parameters
File primary_contigs_list
File reference_fasta
Expand Down Expand Up @@ -119,18 +123,21 @@ workflow GatherSampleEvidence {
File bam_or_cram_index_ = select_first([bam_or_cram_index, bam_or_cram_file + index_ext_])

# move the reads nearby -- handles requester_pays and makes cross-region transfers just once
call LocalizeReads {
if (run_localize_reads) {
call LocalizeReads {
input:
reads_path = bam_or_cram_file,
reads_index = bam_or_cram_index_,
runtime_attr_override = runtime_attr_localize_reads
}
}


if (revise_base) {
call rb.CramToBamReviseBase {
input:
cram_file = LocalizeReads.output_file,
cram_index = LocalizeReads.output_index,
cram_file = select_first([LocalizeReads.output_file, bam_or_cram_file]),
cram_index = select_first([LocalizeReads.output_index, bam_or_cram_index]),
reference_fasta = reference_fasta,
reference_index = reference_index,
contiglist = select_first([primary_contigs_fai]),
Expand All @@ -141,8 +148,8 @@ workflow GatherSampleEvidence {
}
}

File reads_file_ = select_first([CramToBamReviseBase.bam_file, LocalizeReads.output_file])
File reads_index_ = select_first([CramToBamReviseBase.bam_index, LocalizeReads.output_index])
File reads_file_ = select_first([CramToBamReviseBase.bam_file, LocalizeReads.output_file, bam_or_cram_file])
File reads_index_ = select_first([CramToBamReviseBase.bam_index, LocalizeReads.output_index, bam_or_cram_index])

if (collect_coverage || run_melt) {
call cov.CollectCounts {
Expand Down Expand Up @@ -305,6 +312,7 @@ workflow GatherSampleEvidence {
}
}


task LocalizeReads {
input {
File reads_path
Expand Down
5 changes: 5 additions & 0 deletions wdl/GatherSampleEvidenceBatch.wdl
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Expand Up @@ -15,6 +15,10 @@ workflow GatherSampleEvidenceBatch {
Boolean collect_coverage = true
Boolean collect_pesr = true

# Localize reads parameters
# set to true on default, skips localize_reads if set to false
Boolean run_localize_reads = true

# Common parameters
File primary_contigs_list
File reference_fasta
Expand Down Expand Up @@ -136,6 +140,7 @@ workflow GatherSampleEvidenceBatch {
baseline_melt_vcf = baseline_melt_vcf,
baseline_scramble_vcf = baseline_scramble_vcf,
baseline_wham_vcf = baseline_wham_vcf,
run_localize_reads = run_localize_reads,
sv_pipeline_docker = sv_pipeline_docker,
sv_base_mini_docker = sv_base_mini_docker,
samtools_cloud_docker = samtools_cloud_docker,
Expand Down