Skip to content
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

Jump to bottom

Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling #1624

Open
wants to merge 2 commits into
base: dev
Choose a base branch
from
Open

Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling #1624

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
514c81a
Fixes bug
bounlu Aug 16, 2024
1542401
Change to value channel
bounlu Aug 16, 2024
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
2 changes: 1 addition & 1 deletion main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ workflow NFCORE_SAREK {
rt_file = PREPARE_GENOME.out.rt_file

// Tabix indexed vcf files
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
Expand Down
Loading