Skip to content

chore: comply with v2 strict parser syntax #335

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
kelly-sovacool wants to merge 2 commits into
base: main
Choose a base branch
from
Draft

chore: comply with v2 strict parser syntax #335

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6512a45
ci: fix config lint
kelly-sovacool Jun 8, 2026
3b92929
Merge branch 'main' into fix-config-lint
kelly-sovacool Jul 17, 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
4 changes: 2 additions & 2 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
outputDir = 'results'
params {
input = null
outputDir = "${outputDir}"
outputDir = 'results' //"${outputDir}"
tracedir = "${params.outputDir}/pipeline_info"
genome = null // must be listed in conf/genomes.config

Expand Down Expand Up @@ -42,7 +42,7 @@ params {
deeptools_smooth_length = 75
deeptools_corr_method = "spearman" // correlation method for deeptools plotCorrelation: spearman or pearson
deeptools_normalize_using = "RPGC" // set this to "None" if using a spike-in control
deeptools_normalize_samples = deeptools_normalize_using
deeptools_normalize_samples = params.deeptools_normalize_using
deeptools_normalize_input = "RPGC" // this is separate from the above, only for input samples
deeptools_excluded_chroms = "chrM chrX chrY"

Expand Down
Loading