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add optional input parameter length_threshold for paftools.js call #374

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add optional input parameter length_threshold for paftools.js call #374

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8 changes: 6 additions & 2 deletions wdl/tasks/CallAssemblyVariants.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,15 @@ workflow CallAssemblyVariants {
File ref_fasta
String participant_name
String prefix
Int length_threshold = 50000
}

parameter_meta {
asm_fasta: "haploid assembly"
ref_fasta: "reference to which assembly should be aligned"
participant_name: "participant name"
prefix: "prefix for output files"
length_threshold: "By default, paftools.js call ignores alignments 50kb or shorter. For mitochondria, this value should be changed to 10k."
}

call AlignAsPAF {
Expand All @@ -30,7 +32,8 @@ workflow CallAssemblyVariants {
ref_fasta = ref_fasta,
paf = AlignAsPAF.paf,
participant_name = participant_name,
prefix = prefix
prefix = prefix,
length_threshold = length_threshold
}

output {
Expand Down Expand Up @@ -91,6 +94,7 @@ task Paftools {
File paf
String participant_name
String prefix
Int length_threshold

RuntimeAttr? runtime_attr_override
}
Expand All @@ -101,7 +105,7 @@ task Paftools {
command <<<
zcat ~{paf} | \
sort -k6,6 -k8,8n | \
paftools.js call -f ~{ref_fasta} -s ~{participant_name} - \
paftools.js call -L ~{length_threshold} -f ~{ref_fasta} -s ~{participant_name} - \
> ~{prefix}.paftools.vcf
>>>

Expand Down