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Can now specify locus string or a BED file
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@kvg
kvg committed Dec 6, 2024
1 parent 95b1bfc commit b4bda2f
Showing 1 changed file with 95 additions and 26 deletions.
121 changes: 95 additions & 26 deletions wdl/HidiveSample.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,49 +7,68 @@ workflow HidiveSample {
File short_reads_cram
File short_reads_crai

File reference
String locus
String? locus
File? loci

File model
String sample_name

File reference
File ref_fa_with_alt
File ref_fai_with_alt
File ref_cache_tar_gz

Int padding = 500
}

if (defined(locus)) {
call PrepareLocus { input: locus = select_first([locus]) }
}

File bed = select_first([PrepareLocus.bed, loci])

call Fetch {
input:
bam = long_reads_bam,
locus = locus,
loci = bed,
padding = padding,
prefix = sample_name
}

call Rescue {
input:
long_reads_fasta = Fetch.fasta,
short_reads_cram = short_reads_cram,
short_reads_crai = short_reads_crai,
ref_fa_with_alt = ref_fa_with_alt,
ref_fai_with_alt = ref_fai_with_alt,
ref_cache_tar_gz = ref_cache_tar_gz,
prefix = sample_name
}

call Correct {
input:
locus = locus,
loci = bed,
model = model,
reference = reference,
long_reads_bam = long_reads_bam,
short_read_fasta = Rescue.fasta,
prefix = sample_name
}

call Call {
input:
locus = locus,
loci = bed,
reference = reference,
sample_name = sample_name,
aligned_reads_bam = Correct.corrected_bam,
aligned_reads_csi = Correct.corrected_csi,
prefix = sample_name
}

call Consensus {
input:
locus = locus,
loci = bed,
reference = reference,
calls_vcf = Call.calls_vcf,
calls_tbi = Call.calls_tbi,
Expand All @@ -69,10 +88,36 @@ workflow HidiveSample {
}
}

task PrepareLocus {
input {
String locus
}

command <<<
set -euxo pipefail

echo "~{locus}" | \
sed 's/,//g' | \
sed 's/[:\|]/\t/g' | \
sed 's/-/\t/' > locus.bed
>>>

output {
File bed = "locus.bed"
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "1 GB"
cpu: 1
disks: "local-disk 1 SSD"
}
}

task Fetch {
input {
String bam
String locus
File loci
Int padding

String prefix = "out"
Expand All @@ -84,15 +129,15 @@ task Fetch {
command <<<
set -euxo pipefail

hidive fetch -l "~{locus}" -p ~{padding} ~{bam} > ~{prefix}.fa
hidive fetch -l ~{loci} -p ~{padding} ~{bam} > ~{prefix}.fa
>>>

output {
File fasta = "~{prefix}.fa"
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.98"
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "2 GB"
cpu: num_cpus
disks: "local-disk ~{disk_size_gb} SSD"
Expand Down Expand Up @@ -137,7 +182,7 @@ task Rescue {
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:kvg_call"
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "~{memory_gb} GB"
cpu: num_cpus
disks: "local-disk ~{disk_size_gb} SSD"
Expand All @@ -150,7 +195,7 @@ task Correct {
File short_read_fasta
String long_reads_bam

String locus
File loci
File model
File reference

Expand All @@ -165,7 +210,7 @@ task Correct {
command <<<
set -x

hidive correct -l "~{locus}" -m ~{model} ~{long_reads_bam} ~{short_read_fasta} | \
hidive correct -l ~{loci} -m ~{model} ~{long_reads_bam} ~{short_read_fasta} | \
minimap2 -ayYL -x map-hifi ~{reference} - | \
samtools sort --write-index -O BAM -o ~{prefix}.bam
>>>
Expand All @@ -176,7 +221,7 @@ task Correct {
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.98"
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "~{memory_gb} GB"
cpu: num_cpus
disks: "local-disk ~{disk_size_gb} SSD"
Expand All @@ -185,7 +230,7 @@ task Correct {

task Call {
input {
String locus
File loci
File reference
String sample_name

Expand All @@ -203,7 +248,7 @@ task Call {
command <<<
set -x

hidive call -s "~{sample_name}" -l "~{locus}" -r ~{reference} ~{aligned_reads_bam} | bgzip -c > ~{prefix}.vcf.bgz
hidive call -s "~{sample_name}" -l ~{loci} -r ~{reference} ~{aligned_reads_bam} | bgzip -c > ~{prefix}.vcf.bgz
tabix -p vcf ~{prefix}.vcf.bgz
>>>

Expand All @@ -213,7 +258,7 @@ task Call {
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:kvg_call"
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "~{memory_gb} GB"
cpu: num_cpus
disks: "local-disk ~{disk_size_gb} SSD"
Expand All @@ -226,7 +271,8 @@ task Consensus {
File calls_vcf
File calls_tbi

String locus
File loci
String prefix

Int num_cpus = 8
}
Expand All @@ -237,21 +283,44 @@ task Consensus {
command <<<
set -x

LOCUS=$(echo "~{locus}" | sed 's/,//g' | sed 's/|.*//')

samtools faidx ~{reference} ${LOCUS} | bcftools consensus -H 1pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h1.bam
samtools faidx ~{reference} ${LOCUS} | bcftools consensus -H 2pIu ~{calls_vcf} | minimap2 -ayYL -x map-hifi ~{reference} - | samtools sort --write-index -O BAM -o h2.bam
# Process each locus individually and create temporary BAMs
while read -r CHROM START END NAME; do
LOCUS="${CHROM}:${START}-${END}"

# Create per-locus BAMs for haplotype 1
samtools faidx ~{reference} ${LOCUS} | \
bcftools consensus -H 1pIu ~{calls_vcf} | \
minimap2 -ayYL -x map-hifi ~{reference} - | \
samtools sort -O BAM -o tmp.h1.${NAME}.bam

# Create per-locus BAMs for haplotype 2
samtools faidx ~{reference} ${LOCUS} | \
bcftools consensus -H 2pIu ~{calls_vcf} | \
minimap2 -ayYL -x map-hifi ~{reference} - | \
samtools sort -O BAM -o tmp.h2.${NAME}.bam
done < ~{loci}

# Merge all temporary BAMs into final outputs
samtools merge -O BAM ~{prefix}.h1.bam tmp.h1.*.bam
samtools merge -O BAM ~{prefix}.h2.bam tmp.h2.*.bam

# Index final BAMs
samtools index -c ~{prefix}.h1.bam
samtools index -c ~{prefix}.h2.bam

# Cleanup temporary files
rm tmp.h1.*.bam tmp.h2.*.bam
>>>

output {
File h1_bam = "h1.bam"
File h1_csi = "h1.bam.csi"
File h2_bam = "h2.bam"
File h2_csi = "h2.bam.csi"
File h1_bam = "~{prefix}.h1.bam"
File h1_csi = "~{prefix}.h1.bam.csi"
File h2_bam = "~{prefix}.h2.bam"
File h2_csi = "~{prefix}.h2.bam.csi"
}

runtime {
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:kvg_call"
docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
memory: "~{memory_gb} GB"
cpu: num_cpus
disks: "local-disk ~{disk_size_gb} SSD"
Expand Down

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