Skip to content

Output phased variants #141

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

Merged
robert-a-forsyth merged 2 commits into from
Mar 13, 2026
Merged

Output phased variants #141

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
36c449d
add publishdir for phase variants
ljwharbers Mar 12, 2026
8f2a771
renamed phased variants output
ljwharbers Mar 12, 2026
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
6 changes: 4 additions & 2 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,17 +190,19 @@ process {
//

withName: '.*:LONGPHASE_PHASE' {
ext.prefix = { "somatic_smallvariants" }
Copy link

Copilot AI Mar 12, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LONGPHASE_PHASE is used to phase germline/non-somatic SNVs (e.g., normals in subworkflows/local/tumor_normal_happhase.nf and the non-somatic VCF in tumor-only mode). Setting ext.prefix to somatic_smallvariants will label the published phased VCFs as somatic even when they are not, which is misleading for users and downstream tooling. Consider using a neutral prefix (e.g. phased_smallvariants) or include sample/type information in the prefix to accurately reflect the content.

Suggested change
ext.prefix = { "somatic_smallvariants" }
ext.prefix = { "phased_smallvariants" }

Copilot uses AI. Check for mistakes.
ext.args = {
[
meta.platform == 'pb' ? '--pb' : '--ont',
"--indels",
].join(' ').trim()
}
publishDir = [
enabled: false
path: { "${params.outdir}/${meta.id}/variants/phased" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:LONGPHASE_HAPLOTAG' {
ext.prefix = { "${meta.id}_${meta.type}" }
publishDir = [
Expand Down
Loading