Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 1 commit into
base: main
Choose a base branch
from
Draft

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

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 6 additions & 2 deletions wdl/tasks/CallAssemblyVariants.wdl
View file
Open in desktop
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