From 397714cea0f850e726639c60ca094856df99ca10 Mon Sep 17 00:00:00 2001 From: "Mitchell R. Vollger" Date: Thu, 13 Aug 2026 17:55:25 -0700 Subject: [PATCH] feat: default min_frac_accessible to 0.10 FIRE peaks now require >=10% of reads accessible on top of FDR peak calling by default; set min_frac_accessible: 0.0 for the old behavior. Co-Authored-By: Claude Fable 5 --- config/README.md | 4 ++-- workflow/Snakefile | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/README.md b/config/README.md index 2dda19989..01fe3a763 100644 --- a/config/README.md +++ b/config/README.md @@ -57,9 +57,9 @@ Forgo the use of FDR peak calling and instead call peaks for regions with at lea ``` min_per_acc_peak = 0.25 ``` -Apply a percent actuation filter on top of the FDR peak calling. Default is `0.0` for no filter. +Apply a percent actuation filter on top of the FDR peak calling. Default is `0.10`; set to `0.0` for no filter. ``` -min_frac_accessible: 0.0 +min_frac_accessible: 0.10 ``` Process only chromosomes matching this regular expression: ``` diff --git a/workflow/Snakefile b/workflow/Snakefile index dc1e50fdb..967e69371 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -56,7 +56,7 @@ if MIN_PER_ACC_PEAK is None: MIN_PER_ACC_PEAK = 0.0 else: MAX_PEAK_FDR = 1.0 -MIN_FRAC_ACCESSIBLE = config.get("min_frac_accessible", 0) +MIN_FRAC_ACCESSIBLE = config.get("min_frac_accessible", 0.10) # data filtering FILTER_FLAG = config.get("samtools-filter-flag", "260") # 2308