From ad043e39e20820b1a7a70b5f71b01c3e89a2c53c Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Wed, 18 Jun 2025 11:50:04 -0700
Subject: [PATCH 01/17] drop filtering from mosdepth, allow it to only be done
 by the input user controlled input filtering

---
 workflow/rules/coverages.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/coverages.smk b/workflow/rules/coverages.smk
index c354c76cc..9a0aa1394 100644
--- a/workflow/rules/coverages.smk
+++ b/workflow/rules/coverages.smk
@@ -17,7 +17,7 @@ rule genome_bedgraph:
         DEFAULT_ENV
     shell:
         """ 
-        mosdepth -f {input.ref} -t {threads} tmp {input.cram}
+        mosdepth -F 4 -f {input.ref} -t {threads} tmp {input.cram}
         bgzip -cd tmp.per-base.bed.gz \
             | LC_ALL=C sort --parallel={threads} -k1,1 -k2,2n -k3,3n -k4,4  \
             | bgzip -@ {threads} \

From fe6b26f59d1912601994f20f2bab880559d8c3dd Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Fri, 27 Jun 2025 17:56:56 -0700
Subject: [PATCH 02/17] threads

---
 workflow/rules/fire-peaks.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk
index 07d15e0f6..c4471427a 100644
--- a/workflow/rules/fire-peaks.smk
+++ b/workflow/rules/fire-peaks.smk
@@ -141,7 +141,7 @@ rule pileup:
         fofn=temp("temp/{sm}/fire/fire-{v}-pileup.fofn"),
         bed="results/{sm}/{sm}-fire-{v}-pileup.bed.gz",
         tbi="results/{sm}/{sm}-fire-{v}-pileup.bed.gz.tbi",
-    threads: 4
+    threads: 8
     conda:
         DEFAULT_ENV
     shell:

From 07432a98a9c7666e616ea5cba08aaa6416afde32 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Sat, 28 Jun 2025 21:11:40 -0700
Subject: [PATCH 03/17] avoid rerunning when not needed

---
 workflow/Snakefile | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index f36e0da1c..d8b132cf1 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -130,12 +130,7 @@ rule all:
         # coverage information
         expand(rules.coverage.output, sm=MANIFEST.index, v=VERSION),
         expand(rules.exclude_from_shuffle.output, sm=MANIFEST.index, v=VERSION),
-        expand(rules.unreliable_coverage_regions.output, sm=MANIFEST.index, v=VERSION),
-        expand(
-            rules.pileup.output.bed,
-            sm=MANIFEST.index,
-            v=VERSION,
-        ),
+        expand(rules.unreliable_coverage_regions.output.bed, sm=MANIFEST.index, v=VERSION),
         # model results
         expand(rules.fire.output.cram, sm=MANIFEST.index, v=VERSION),
         expand(rules.fire_sites.output, sm=MANIFEST.index, v=VERSION),

From 49a81725b363ac5657232b1c24c1a1919307ddc8 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Tue, 4 Nov 2025 10:14:28 -0500
Subject: [PATCH 04/17] plot legends

---
 workflow/scripts/hap-diffs.R | 259 ++++++++++++++++++-----------------
 1 file changed, 131 insertions(+), 128 deletions(-)

diff --git a/workflow/scripts/hap-diffs.R b/workflow/scripts/hap-diffs.R
index c21934805..49236d0b6 100644
--- a/workflow/scripts/hap-diffs.R
+++ b/workflow/scripts/hap-diffs.R
@@ -4,23 +4,23 @@ library(scales)
 library(ggforce)
 library(cowplot)
 library(dplyr)
-#library(splitstackshape)
-#library(ggridges)
-#library(IRanges)
+# library(splitstackshape)
+# library(ggridges)
+# library(IRanges)
 library(ggrepel)
-#library(ggnewscale)
-#library(ggside)
+# library(ggnewscale)
+# library(ggside)
 library(glue)
-#library("tidylog", warn.conflicts = FALSE)
-#library(patchwork)
-#library(ggh4x)
+# library("tidylog", warn.conflicts = FALSE)
+# library(patchwork)
+# library(ggh4x)
 library(tools)
-#library(purrr)
-#library(reticulate)
+# library(purrr)
+# library(reticulate)
 library(ggpubr)
-#library(weights)
-#library(karyoploteR)
-#library(zoo)
+# library(weights)
+# library(karyoploteR)
+# library(zoo)
 library(scales)
 library(ggplot2)
 library(ggforce)
@@ -28,61 +28,63 @@ library(grid)
 options(scipen = 999)
 
 
-Red="#c1272d"
-Indigo="#0000a7"
-Yellow="#eecc16"
-Teal="#008176"
-Gray="#b3b3b3"
-FONT_SIZE=8
-MODEL_COLORS = c(PacBio=Indigo, 
-    CNN=Red,  
-    XGB=Yellow,
-    GMM=Teal,
-    IPD=Gray,
-    SEMI="purple",
-    Revio="#f41c90" # black
+Red <- "#c1272d"
+Indigo <- "#0000a7"
+Yellow <- "#eecc16"
+Teal <- "#008176"
+Gray <- "#b3b3b3"
+FONT_SIZE <- 8
+MODEL_COLORS <- c(
+    PacBio = Indigo,
+    CNN = Red,
+    XGB = Yellow,
+    GMM = Teal,
+    IPD = Gray,
+    SEMI = "purple",
+    Revio = "#f41c90" # black
 )
 
-my_ggsave <- function(file, ...){
-    file = glue(file)
+my_ggsave <- function(file, ...) {
+    file <- glue(file)
     print(file)
-    ext = file_ext(file)
-    file_without_ext = tools::file_path_sans_ext(file)
-    ggsave(glue("tmp.{ext}"), bg='transparent', ...)
-    cmd = glue("cp tmp.{ext} {file}")
-    fwrite(last_plot()$data, file=file_without_ext + ".tbl.gz", sep="\t")
+    ext <- file_ext(file)
+    file_without_ext <- tools::file_path_sans_ext(file)
+    ggsave(glue("tmp.{ext}"), bg = "transparent", ...)
+    cmd <- glue("cp tmp.{ext} {file}")
+    fwrite(last_plot()$data, file = file_without_ext + ".tbl.gz", sep = "\t")
     print(cmd)
     system(cmd)
 }
 
-my_grid = function(...){
-    theme_minimal_grid(font_size=FONT_SIZE, ...)
-} 
+my_grid <- function(...) {
+    theme_minimal_grid(font_size = FONT_SIZE, ...)
+}
 
-my_hgrid = function(...){
-    theme_minimal_hgrid(font_size=FONT_SIZE, ...)
-} 
+my_hgrid <- function(...) {
+    theme_minimal_hgrid(font_size = FONT_SIZE, ...)
+}
 
-my_vgrid = function(...){
-    theme_minimal_vgrid(font_size=FONT_SIZE, ...)
-} 
+my_vgrid <- function(...) {
+    theme_minimal_vgrid(font_size = FONT_SIZE, ...)
+}
 
 reverselog_trans <- function(base = exp(1)) {
     trans <- function(x) -log(x, base)
     inv <- function(x) base^(-x)
-    trans_new(paste0("reverselog-", format(base)), trans, inv, 
-              log_breaks(base = base), 
-              domain = c(1e-100, Inf))
+    trans_new(paste0("reverselog-", format(base)), trans, inv,
+        log_breaks(base = base),
+        domain = c(1e-100, Inf)
+    )
 }
 
 scientific_10 <- function(x) {
-    is_one = as.numeric(x) == 1
-    text = gsub("e", " %*% 10^", scales::scientific_format()(x))
+    is_one <- as.numeric(x) == 1
+    text <- gsub("e", " %*% 10^", scales::scientific_format()(x))
     print(text)
-    text = str_remove(text, "^1 %\\*% ") # remove leading one 
+    text <- str_remove(text, "^1 %\\*% ") # remove leading one
     print(text)
-    text[is_one] = "10^0"
-    rtn = parse(text=text)
+    text[is_one] <- "10^0"
+    rtn <- parse(text = text)
     rtn
 }
 
@@ -91,17 +93,17 @@ scientific_10 <- function(x) {
 # SCRIPT
 #
 #
-p_threshold=0.05
-in_file=snakemake@input[[1]]
-out_file_1=snakemake@output[[1]]
-out_file_2=snakemake@output[[2]]
-out_file_3=snakemake@output[[3]]
-out_file_4=snakemake@output[[4]]
+p_threshold <- 0.05
+in_file <- snakemake@input[[1]]
+out_file_1 <- snakemake@output[[1]]
+out_file_2 <- snakemake@output[[2]]
+out_file_3 <- snakemake@output[[3]]
+out_file_4 <- snakemake@output[[4]]
 
 
-df=fread(in_file) %>%
+df <- fread(in_file) %>%
     mutate_at(
-        c("fire_coverage_H1","fire_coverage_H2","coverage_H1","coverage_H2"),
+        c("fire_coverage_H1", "fire_coverage_H2", "coverage_H1", "coverage_H2"),
         as.numeric
     ) %>%
     filter(pass_coverage) %>%
@@ -112,8 +114,8 @@ df=fread(in_file) %>%
         !is.na(coverage_H2),
     ) %>%
     mutate(
-        st=peak_start,
-        en=peak_end,
+        st = peak_start,
+        en = peak_end,
         `#ct` = `#chrom`,
     ) %>%
     data.table()
@@ -121,30 +123,30 @@ df=fread(in_file) %>%
 print("Before coverage filter")
 print(nrow(df))
 
-# continue 
-df$hap1_frac_acc = df$fire_coverage_H1/df$coverage_H1
-df$hap2_frac_acc = df$fire_coverage_H2/df$coverage_H2
-df$autosome = "Autosome"
-df[`#chrom` == "chrY"]$autosome = "chrY"
-df[`#chrom` == "chrX"]$autosome = "chrX"
+# continue
+df$hap1_frac_acc <- df$fire_coverage_H1 / df$coverage_H1
+df$hap2_frac_acc <- df$fire_coverage_H2 / df$coverage_H2
+df$autosome <- "Autosome"
+df[`#chrom` == "chrY"]$autosome <- "chrY"
+df[`#chrom` == "chrX"]$autosome <- "chrX"
 
 # filter by coverage
-sd = 3
-cov = median(df$coverage)
-my_min_cov = max(cov*0.5 - sd * sqrt(cov*0.5), 10)
-my_max_cov = cov*0.5 + sd * sqrt(cov*0.5)
-#my_min_cov = 10
-#my_max_cov = median(df$coverage)
+sd <- 3
+cov <- median(df$coverage)
+my_min_cov <- max(cov * 0.5 - sd * sqrt(cov * 0.5), 10)
+my_max_cov <- cov * 0.5 + sd * sqrt(cov * 0.5)
+# my_min_cov = 10
+# my_max_cov = median(df$coverage)
 
-#print(glue("min_cov={my_min_cov} max_cov={my_max_cov} cov={cov}"))
+# print(glue("min_cov={my_min_cov} max_cov={my_max_cov} cov={cov}"))
 
-pdf = df %>%
+pdf <- df %>%
     filter(coverage_H1 > 0 & coverage_H2 > 0) %>%
     mutate(
         min_cov = my_min_cov,
         max_cov = my_max_cov,
     ) %>%
-    filter(autosome != "chrY" ) %>%
+    filter(autosome != "chrY") %>%
     filter(coverage_H1 > min_cov & coverage_H2 > min_cov) %>%
     filter(coverage_H1 < max_cov & coverage_H2 < max_cov) %>%
     mutate(
@@ -157,7 +159,7 @@ pdf = df %>%
 print("After coverage filter")
 print(nrow(pdf))
 
-if(nrow(pdf)== 0){
+if (nrow(pdf) == 0) {
     system(glue("touch {out_file_1}"))
     system(glue("touch {out_file_2}"))
     system(glue("touch {out_file_3}"))
@@ -165,21 +167,21 @@ if(nrow(pdf)== 0){
     quit()
 }
 
-pdf = pdf %>%
+pdf <- pdf %>%
     filter(
-      hap1_acc >= 0,
-      hap1_nacc >= 0,
-      hap2_acc >= 0,
-      hap2_nacc >= 0,
+        hap1_acc >= 0,
+        hap1_nacc >= 0,
+        hap2_acc >= 0,
+        hap2_nacc >= 0,
     ) %>%
     rowwise() %>%
     mutate(
-        p_value=fisher.test(matrix(c(hap1_acc, hap1_nacc, hap2_acc, hap2_nacc),nrow=2))$p.value
+        p_value = fisher.test(matrix(c(hap1_acc, hap1_nacc, hap2_acc, hap2_nacc), nrow = 2))$p.value
     ) %>%
     ungroup() %>%
     group_by(autosome) %>%
     mutate(
-        p_adjust = p.adjust(p_value, method="BH"),
+        p_adjust = p.adjust(p_value, method = "BH"),
     ) %>%
     select(!starts_with("V")) %>%
     mutate(
@@ -194,66 +196,67 @@ print("After p-value adjustment")
 print(nrow(pdf %>% filter(p_adjust <= p_threshold)))
 
 # make the plots
-tdf = pdf 
+tdf <- pdf
 
 tdf %>%
-    ggplot(aes(x=hap1_frac_acc, y=hap2_frac_acc)) +
-    stat_cor(size=2) +
-    geom_hex(bins=75) +
-    geom_abline(aes(intercept=0, slope=1), linetype="dashed")+
-    scale_fill_distiller("", palette = "Spectral", trans="log10") +
-    scale_x_continuous("Paternal accessibility", labels=percent) +
-    scale_y_continuous("Maternal accessibility", labels=percent) +
-    #annotation_logticks(sides="lb") +
-    facet_wrap(~autosome, ncol=2)+
+    ggplot(aes(x = hap1_frac_acc, y = hap2_frac_acc)) +
+    stat_cor(size = 2) +
+    geom_hex(bins = 75) +
+    geom_abline(aes(intercept = 0, slope = 1), linetype = "dashed") +
+    scale_fill_distiller("", palette = "Spectral", trans = "log10") +
+    scale_x_continuous("H1 accessibility", labels = percent) +
+    scale_y_continuous("H2 accessibility", labels = percent) +
+    # annotation_logticks(sides="lb") +
+    facet_wrap(~autosome, ncol = 2) +
     my_grid()
-my_ggsave(out_file_1, height=3, width=6)
+my_ggsave(out_file_1, height = 3, width = 6)
 
-cor_p_threshold = max(tdf[p_adjust <= p_threshold & !is.na(p_value) & !is.na(p_adjust) ]$p_value)
+cor_p_threshold <- max(tdf[p_adjust <= p_threshold & !is.na(p_value) & !is.na(p_adjust)]$p_value)
 print(cor_p_threshold)
-y_lim = ceiling(max(max(-log10(tdf$p_value)), max(-log10(tdf$p_adjust)))) 
-y_by = 1 
-if(y_lim > 10){
-    y_by = 2
+y_lim <- ceiling(max(max(-log10(tdf$p_value)), max(-log10(tdf$p_adjust))))
+y_by <- 1
+if (y_lim > 10) {
+    y_by <- 2
 }
 # add p-value col, volcano plot
-n=comma(nrow(tdf))
-p = tdf %>%
-    ggplot(aes(x=diff, y=p_value)) +
-    geom_hex(bins=100) + scale_fill_distiller("", palette = "Spectral", trans="log10") +
-    geom_hline(aes(yintercept=(p_threshold)), linetype="dashed", color="darkblue")+
-    geom_hline(aes(yintercept=(cor_p_threshold)), linetype="dashed", color="darkred")+
-    facet_wrap(~autosome, ncol=2)+
-    scale_x_continuous("Difference between paternal and maternal accessibility", labels=percent) +
+n <- comma(nrow(tdf))
+p <- tdf %>%
+    ggplot(aes(x = diff, y = p_value)) +
+    geom_hex(bins = 100) +
+    scale_fill_distiller("", palette = "Spectral", trans = "log10") +
+    geom_hline(aes(yintercept = (p_threshold)), linetype = "dashed", color = "darkblue") +
+    geom_hline(aes(yintercept = (cor_p_threshold)), linetype = "dashed", color = "darkred") +
+    facet_wrap(~autosome, ncol = 2) +
+    scale_x_continuous("Difference between H1 and H2 accessibility", labels = percent) +
     scale_y_continuous(
-        glue("p-value   (n = {n})"), 
-        #labels=comma,
-        breaks=10**(-seq(0, y_lim, y_by)),
-        minor_breaks=10**(-seq(0, y_lim, 0.1)),
-        trans=reverselog_trans(10),
-        labels=scientific_10,
-    ) + 
+        glue("p-value   (n = {n})"),
+        # labels=comma,
+        breaks = 10**(-seq(0, y_lim, y_by)),
+        minor_breaks = 10**(-seq(0, y_lim, 0.1)),
+        trans = reverselog_trans(10),
+        labels = scientific_10,
+    ) +
     my_grid()
-my_ggsave(out_file_2, height=3, width=5)
+my_ggsave(out_file_2, height = 3, width = 5)
 
-# save the table 
-fwrite(tdf[tdf$p_value <= 1], out_file_3, sep="\t")
+# save the table
+fwrite(tdf[tdf$p_value <= 1], out_file_3, sep = "\t")
 # save the bed9
-# 
+#
 tdf %>%
     mutate(
-        score = pmin(round(1/p_value), 1000),
+        score = pmin(round(1 / p_value), 1000),
         name = paste0(
-            round(p_value,5), "_",
-            round(100*hap1_frac_acc,2), "_",
-            round(100*hap2_frac_acc,2)
+            round(p_value, 5), "_",
+            round(100 * hap1_frac_acc, 2), "_",
+            round(100 * hap2_frac_acc, 2)
         ),
-        tst=st+1,
-        ten=case_when(
-            p_value<=p_threshold ~ en - 1,
-            TRUE ~ st+2
+        tst = st + 1,
+        ten = case_when(
+            p_value <= p_threshold ~ en - 1,
+            TRUE ~ st + 2
         ),
-        strand=".",
+        strand = ".",
         color = case_when(
             hap1_frac_acc > hap2_frac_acc & p_value > p_threshold ~ "0,0,100",
             hap1_frac_acc > hap2_frac_acc ~ "0,0,255",
@@ -263,4 +266,4 @@ tdf %>%
         )
     ) %>%
     select(c("#chrom", "st", "en", "name", "score", "strand", "tst", "ten", "color")) %>%
-    fwrite(out_file_4, sep="\t", quote=F, na=".", row.names=F)
+    fwrite(out_file_4, sep = "\t", quote = F, na = ".", row.names = F)

From cdea97c57b14f87bb8610735e96c6764b93257aa Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Thu, 6 Nov 2025 10:33:21 -0500
Subject: [PATCH 05/17] .

---
 pixi.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index 431ab05e7..a09825f9b 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,4 +1,4 @@
-[project]
+[workspace]
 authors = ["Mitchell Robert Vollger <mrvollger@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 description = "Add a short description here"

From 28dd67735673f21420364df85eeb3ba7ba9b1e2d Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Wed, 12 Nov 2025 14:06:51 -0700
Subject: [PATCH 06/17] stop using awscli

---
 pixi.lock | 3350 ++++++++++-------------------------------------------
 pixi.toml |   10 +-
 2 files changed, 611 insertions(+), 2749 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index d798a10b3..5907f8438 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,4 +1,4 @@
-version: 5
+version: 6
 environments:
   default:
     channels:
@@ -14,19 +14,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/archspec-0.2.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.7.31-hd5d0ea3_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.7.4-hae4d56a_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.29-hb9d3cd8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.19-h2bff981_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.4.3-h6c1f5b1_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.10-hf2c527e_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.20-hc9e6898_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.10.7-hfbb250a_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.6.7-h7f2cdf9_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.19-h2bff981_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.20-h2bff981_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/awscli-2.22.0-py312h7900ff3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/awscrt-0.22.0-py312hce51685_6.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/black-24.10.0-py312h7900ff3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/boltons-24.0.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h2ec8cdc_2.conda
@@ -52,7 +39,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/connection_pool-0.0.3-pyhd3deb0d_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-43.0.1-py312hda17c39_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/datrie-0.8.2-py312h66e93f0_8.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyhd81877a_7.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/icu-73.2-hf5e326d_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/immutables-0.21-py312h66e93f0_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/immutables-0.21-py312hb553811_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.4-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonpatch-1.33-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/jsonpointer-3.0.0-py312h7900ff3_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/jsonpointer-3.0.0-py312hb401068_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.23.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2024.10.1-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_core-5.7.2-pyh31011fe_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
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+- conda: https://conda.anaconda.org/conda-forge/noarch/slack-sdk-3.33.3-pyha770c72_0.conda
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   noarch: python
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+- conda: https://conda.anaconda.org/conda-forge/noarch/smart_open-7.0.5-pyhd8ed1ab_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/smmap-5.0.0-pyhd8ed1ab_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakefmt-0.10.2-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-8.21.0-hdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-0.11.2-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-jobstep-0.2.1-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.17.4-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.3.2-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.1.0-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-3.3.0-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-8.21.0-pyhdfd78af_0.tar.bz2
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+- conda: https://conda.anaconda.org/conda-forge/noarch/tabulate-0.9.0-pyhd8ed1ab_1.tar.bz2
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/taplo-0.9.3-h53e704d_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/taplo-0.9.3-hf3953a5_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/throttler-1.2.2-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/tk-8.6.13-h1abcd95_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.1.0-pyhff2d567_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/toposort-1.10-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/truststore-0.10.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.13.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-slim-0.13.0-pyhff2d567_0.conda
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   md5: 5fcd867cf0b4498002731d44621c0b58
   depends:
@@ -5487,13 +3489,7 @@ packages:
   - pkg:pypi/typer-slim?source=hash-mapping
   size: 43166
   timestamp: 1731015659531
-- kind: conda
-  name: typer-slim-standard
-  version: 0.13.0
-  build: hd8ed1ab_0
-  subdir: noarch
-  noarch: generic
-  url: https://conda.anaconda.org/conda-forge/noarch/typer-slim-standard-0.13.0-hd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-slim-standard-0.13.0-hd8ed1ab_0.conda
   sha256: 402d1c872adb1dda436d563e03280750419367fb808a9ee7811f1335f218e8bc
   md5: fe8bb6071bf1c47b38bc65f848847059
   depends:
@@ -5505,13 +3501,8 @@ packages:
   purls: []
   size: 48480
   timestamp: 1731015660139
-- kind: conda
-  name: typing-extensions
-  version: 4.12.2
-  build: hd8ed1ab_0
-  subdir: noarch
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.12.2-hd8ed1ab_0.conda
   noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.12.2-hd8ed1ab_0.conda
   sha256: d3b9a8ed6da7c9f9553c5fd8a4fca9c3e0ab712fa5f497859f82337d67533b73
   md5: 52d648bd608f5737b123f510bb5514b5
   depends:
@@ -5521,13 +3512,7 @@ packages:
   purls: []
   size: 10097
   timestamp: 1717802659025
-- kind: conda
-  name: typing_extensions
-  version: 4.12.2
-  build: pyha770c72_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.12.2-pyha770c72_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.12.2-pyha770c72_0.conda
   sha256: 0fce54f8ec3e59f5ef3bb7641863be4e1bf1279623e5af3d3fa726e8f7628ddb
   md5: ebe6952715e1d5eb567eeebf25250fa7
   depends:
@@ -5538,26 +3523,14 @@ packages:
   - pkg:pypi/typing-extensions?source=hash-mapping
   size: 39888
   timestamp: 1717802653893
-- kind: conda
-  name: tzdata
-  version: 2024b
-  build: hc8b5060_0
-  subdir: noarch
-  noarch: generic
-  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda
   sha256: 4fde5c3008bf5d2db82f2b50204464314cc3c91c1d953652f7bd01d9e52aefdf
   md5: 8ac3367aafb1cc0a068483c580af8015
   license: LicenseRef-Public-Domain
   purls: []
   size: 122354
   timestamp: 1728047496079
-- kind: conda
-  name: ubiquerg
-  version: 0.8.0
-  build: pyhd8ed1ab_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/ubiquerg-0.8.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ubiquerg-0.8.0-pyhd8ed1ab_0.conda
   sha256: ad56b48194d59a640be34432b0acdebe6e5520a86f5e2d0eabab567fc4976d53
   md5: 41408dc37271d5d0f99e2e10336cf40d
   depends:
@@ -5569,13 +3542,7 @@ packages:
   - pkg:pypi/ubiquerg?source=hash-mapping
   size: 20698
   timestamp: 1719492750373
-- kind: conda
-  name: urllib3
-  version: 1.26.19
-  build: pyhd8ed1ab_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.19-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.19-pyhd8ed1ab_0.conda
   sha256: 543ebab5241418a4e0d4d9e356ef13e4361504810a067a01481660bb35eb5643
   md5: 6bb37c314b3cc1515dcf086ffe01c46e
   depends:
@@ -5588,13 +3555,7 @@ packages:
   - pkg:pypi/urllib3?source=hash-mapping
   size: 115125
   timestamp: 1718728467518
-- kind: conda
-  name: veracitools
-  version: 0.1.3
-  build: py_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/veracitools-0.1.3-py_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/veracitools-0.1.3-py_0.tar.bz2
   sha256: f2222d612da9a362b8ff13c8411faa8077dff54fa2e71813c341aa0823b41b24
   md5: f2c8d44ea78cf639ab4810aedba43ab5
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@@ -5606,30 +3567,7 @@ packages:
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   size: 6108
   timestamp: 1572717780817
-- kind: conda
-  name: wcwidth
-  version: 0.2.13
-  build: pyhd8ed1ab_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.13-pyhd8ed1ab_0.conda
-  sha256: b6cd2fee7e728e620ec736d8dfee29c6c9e2adbd4e695a31f1d8f834a83e57e3
-  md5: 68f0738df502a14213624b288c60c9ad
-  depends:
-  - python >=3.8
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/wcwidth?source=hash-mapping
-  size: 32709
-  timestamp: 1704731373922
-- kind: conda
-  name: wrapt
-  version: 1.16.0
-  build: py312h66e93f0_1
-  build_number: 1
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.16.0-py312h66e93f0_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.16.0-py312h66e93f0_1.conda
   sha256: 3a15a399eb61a999f0f14b4d243acc14e2dff1ead92ef52fcff30c84be89b21c
   md5: 2eebcffe80e2a7bb2f0a77e621a7f124
   depends:
@@ -5643,13 +3581,7 @@ packages:
   - pkg:pypi/wrapt?source=hash-mapping
   size: 62624
   timestamp: 1724958046744
-- kind: conda
-  name: wrapt
-  version: 1.16.0
-  build: py312hb553811_1
-  build_number: 1
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/wrapt-1.16.0-py312hb553811_1.conda
+- conda: https://conda.anaconda.org/conda-forge/osx-64/wrapt-1.16.0-py312hb553811_1.conda
   sha256: 31e3fdd934cdb8ac47764d1daf13edddd7844a17b229e8ef438fc16e06576b00
   md5: 6385725172f8712d54b5af6b86bf8236
   depends:
@@ -5662,12 +3594,7 @@ packages:
   - pkg:pypi/wrapt?source=hash-mapping
   size: 58290
   timestamp: 1724958107514
-- kind: conda
-  name: xz
-  version: 5.2.6
-  build: h166bdaf_0
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
   sha256: 03a6d28ded42af8a347345f82f3eebdd6807a08526d47899a42d62d319609162
   md5: 2161070d867d1b1204ea749c8eec4ef0
   depends:
@@ -5676,39 +3603,14 @@ packages:
   purls: []
   size: 418368
   timestamp: 1660346797927
-- kind: conda
-  name: xz
-  version: 5.2.6
-  build: h775f41a_0
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2
   sha256: eb09823f34cc2dd663c0ec4ab13f246f45dcd52e5b8c47b9864361de5204a1c8
   md5: a72f9d4ea13d55d745ff1ed594747f10
   license: LGPL-2.1 and GPL-2.0
   purls: []
   size: 238119
   timestamp: 1660346964847
-- kind: conda
-  name: yaml
-  version: 0.2.5
-  build: h0d85af4_2
-  build_number: 2
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h0d85af4_2.tar.bz2
-  sha256: 5301417e2c8dea45b401ffee8df3957d2447d4ce80c83c5ff151fc6bfe1c4148
-  md5: d7e08fcf8259d742156188e8762b4d20
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 84237
-  timestamp: 1641347062780
-- kind: conda
-  name: yaml
-  version: 0.2.5
-  build: h7f98852_2
-  build_number: 2
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
   sha256: a4e34c710eeb26945bdbdaba82d3d74f60a78f54a874ec10d373811a5d217535
   md5: 4cb3ad778ec2d5a7acbdf254eb1c42ae
   depends:
@@ -5718,12 +3620,15 @@ packages:
   purls: []
   size: 89141
   timestamp: 1641346969816
-- kind: conda
-  name: yaml-cpp
-  version: 0.8.0
-  build: h59595ed_0
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h59595ed_0.conda
+- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h0d85af4_2.tar.bz2
+  sha256: 5301417e2c8dea45b401ffee8df3957d2447d4ce80c83c5ff151fc6bfe1c4148
+  md5: d7e08fcf8259d742156188e8762b4d20
+  license: MIT
+  license_family: MIT
+  purls: []
+  size: 84237
+  timestamp: 1641347062780
+- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h59595ed_0.conda
   sha256: a65bb5284369e548a15a44b14baf1f7ac34fa4718d7d987dd29032caba2ecf20
   md5: 965eaacd7c18eb8361fd12bb9e7a57d7
   depends:
@@ -5734,12 +3639,7 @@ packages:
   purls: []
   size: 204867
   timestamp: 1695710312002
-- kind: conda
-  name: yaml-cpp
-  version: 0.8.0
-  build: he965462_0
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-he965462_0.conda
+- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-he965462_0.conda
   sha256: 6e5e4afa1011a1ad5a734e895b8d2b2ad0fbc9ef6538aac8f852b33b2ebe44a8
   md5: 1bb3addc859ed1338370da6e2996ef47
   depends:
@@ -5749,13 +3649,7 @@ packages:
   purls: []
   size: 130328
   timestamp: 1695710502498
-- kind: conda
-  name: yte
-  version: 1.5.4
-  build: pyha770c72_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/yte-1.5.4-pyha770c72_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.5.4-pyha770c72_0.conda
   sha256: 772972b3e2ebeeb6dd2a3209b95c99b23d21c6657ebf2f758f9e63ccfa28dfc8
   md5: f4d2f4a372be452baebf8dbdcd9892ed
   depends:
@@ -5769,13 +3663,7 @@ packages:
   - pkg:pypi/yte?source=hash-mapping
   size: 14311
   timestamp: 1702295254855
-- kind: conda
-  name: zipp
-  version: 3.21.0
-  build: pyhd8ed1ab_0
-  subdir: noarch
-  noarch: python
-  url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_0.conda
   sha256: 232a30e4b0045c9de5e168dda0328dc0e28df9439cdecdfb97dd79c1c82c4cec
   md5: fee389bf8a4843bd7a2248ce11b7f188
   depends:
@@ -5786,18 +3674,13 @@ packages:
   - pkg:pypi/zipp?source=hash-mapping
   size: 21702
   timestamp: 1731262194278
-- kind: conda
-  name: zstandard
-  version: 0.23.0
-  build: py312h7122b0e_1
-  build_number: 1
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py312h7122b0e_1.conda
-  sha256: 2685dde42478fae0780fba5d1f8a06896a676ae105f215d32c9f9e76f3c6d8fd
-  md5: bd132ba98f3fc0a6067f355f8efe4cb6
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312hef9b889_1.conda
+  sha256: b97015e146437283f2213ff0e95abdc8e2480150634d81fbae6b96ee09f5e50b
+  md5: 8b7069e9792ee4e5b4919a7a306d2e67
   depends:
-  - __osx >=10.13
+  - __glibc >=2.17,<3.0.a0
   - cffi >=1.11
+  - libgcc >=13
   - python >=3.12,<3.13.0a0
   - python_abi 3.12.* *_cp312
   - zstd >=1.5.6,<1.5.7.0a0
@@ -5806,21 +3689,14 @@ packages:
   license_family: BSD
   purls:
   - pkg:pypi/zstandard?source=hash-mapping
-  size: 410873
-  timestamp: 1725305688706
-- kind: conda
-  name: zstandard
-  version: 0.23.0
-  build: py312hef9b889_1
-  build_number: 1
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312hef9b889_1.conda
-  sha256: b97015e146437283f2213ff0e95abdc8e2480150634d81fbae6b96ee09f5e50b
-  md5: 8b7069e9792ee4e5b4919a7a306d2e67
+  size: 419552
+  timestamp: 1725305670210
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py312h7122b0e_1.conda
+  sha256: 2685dde42478fae0780fba5d1f8a06896a676ae105f215d32c9f9e76f3c6d8fd
+  md5: bd132ba98f3fc0a6067f355f8efe4cb6
   depends:
-  - __glibc >=2.17,<3.0.a0
+  - __osx >=10.13
   - cffi >=1.11
-  - libgcc >=13
   - python >=3.12,<3.13.0a0
   - python_abi 3.12.* *_cp312
   - zstd >=1.5.6,<1.5.7.0a0
@@ -5829,30 +3705,9 @@ packages:
   license_family: BSD
   purls:
   - pkg:pypi/zstandard?source=hash-mapping
-  size: 419552
-  timestamp: 1725305670210
-- kind: conda
-  name: zstd
-  version: 1.5.6
-  build: h915ae27_0
-  subdir: osx-64
-  url: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
-  sha256: efa04a98cb149643fa54c4dad5a0179e36a5fbc88427ea0eec88ceed87fd0f96
-  md5: 4cb2cd56f039b129bb0e491c1164167e
-  depends:
-  - __osx >=10.9
-  - libzlib >=1.2.13,<2.0.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  purls: []
-  size: 498900
-  timestamp: 1714723303098
-- kind: conda
-  name: zstd
-  version: 1.5.6
-  build: ha6fb4c9_0
-  subdir: linux-64
-  url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
+  size: 410873
+  timestamp: 1725305688706
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
   sha256: c558b9cc01d9c1444031bd1ce4b9cff86f9085765f17627a6cd85fc623c8a02b
   md5: 4d056880988120e29d75bfff282e0f45
   depends:
@@ -5864,3 +3719,14 @@ packages:
   purls: []
   size: 554846
   timestamp: 1714722996770
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
+  sha256: efa04a98cb149643fa54c4dad5a0179e36a5fbc88427ea0eec88ceed87fd0f96
+  md5: 4cb2cd56f039b129bb0e491c1164167e
+  depends:
+  - __osx >=10.9
+  - libzlib >=1.2.13,<2.0.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 498900
+  timestamp: 1714723303098
diff --git a/pixi.toml b/pixi.toml
index a09825f9b..6ae4ccb51 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -16,13 +16,9 @@ test-data = { cmd = [
     "-p",
     "fire-test-data",
     "&&",
-    "aws",
-    "s3",
-    "--no-sign-request",
+    "rclone",
     "sync",
-    "--endpoint-url",
-    "https://s3.kopah.orci.washington.edu",
-    "s3://stergachis/public/FIRE/test-data",
+    ":s3,env_auth=false,provider=Other,endpoint=s3.kopah.orci.washington.edu:stergachis/public/FIRE/test-data",
     "fire-test-data/",
 ] }
 test = { cmd = [
@@ -63,7 +59,7 @@ snakemake = "==8.21"
 snakemake-executor-plugin-slurm = ">=0.11.2"
 snakefmt = "*"
 ruff = "*"
-awscli = "2.22.*"
+rclone = "*"
 taplo = "*"
 
 [pypi-dependencies]

From 82ad92d6e67ece6ca510d3e4766cb7e0ab38ab90 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmai.com>
Date: Wed, 12 Nov 2025 14:10:58 -0700
Subject: [PATCH 07/17] stop using awscli

---
 pixi.lock | 4579 ++++++++++++++++++++++++++---------------------------
 1 file changed, 2217 insertions(+), 2362 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 5907f8438..f74a90fde 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -8,366 +8,369 @@ environments:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/archspec-0.2.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/archspec-0.2.5-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-24.2.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/black-24.10.0-py312h7900ff3_0.conda
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+  - python >=3.9
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   license: MIT
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+  sha256: 4b3ab84e499b52ede2e6b5164cc5f4137952e11ce1e30a376a3f5e78c643fb64
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+  - conda-libmamba-solver >=25.4.0
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@@ -916,23 +880,21 @@ packages:
   - truststore >=0.8.0
   - zstandard >=0.19.0
   constrains:
-  - conda-build >=24.3
-  - conda-env >=2.6
+  - conda-build >=25.9
   - conda-content-trust >=0.1.1
+  - conda-env >=2.6
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   license_family: BSD
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/conda-24.9.2-py312hb401068_0.conda
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+  size: 1206330
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+- conda: https://conda.anaconda.org/conda-forge/osx-64/conda-25.9.1-py312hb401068_0.conda
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   - distro >=1.5.0
   - frozendict >=2.4.2
@@ -951,15 +913,13 @@ packages:
   - truststore >=0.8.0
   - zstandard >=0.19.0
   constrains:
-  - conda-build >=24.3
   - conda-content-trust >=0.1.1
+  - conda-build >=25.9
   - conda-env >=2.6
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   license_family: BSD
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-  - pkg:pypi/conda?source=hash-mapping
-  size: 1163211
-  timestamp: 1729155314354
+  size: 1208983
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 - conda: https://conda.anaconda.org/conda-forge/noarch/conda-inject-1.3.2-pyhd8ed1ab_0.conda
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@@ -968,60 +928,52 @@ packages:
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   license_family: MIT
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   size: 10327
   timestamp: 1717043667069
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2
-  sha256: eb09823f34cc2dd663c0ec4ab13f246f45dcd52e5b8c47b9864361de5204a1c8
-  md5: a72f9d4ea13d55d745ff1ed594747f10
-  license: LGPL-2.1 and GPL-2.0
-  purls: []
-  size: 238119
-  timestamp: 1660346964847
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
-  sha256: a4e34c710eeb26945bdbdaba82d3d74f60a78f54a874ec10d373811a5d217535
-  md5: 4cb3ad778ec2d5a7acbdf254eb1c42ae
-  depends:
-  - libgcc-ng >=9.4.0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 89141
-  timestamp: 1641346969816
-- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h0d85af4_2.tar.bz2
-  sha256: 5301417e2c8dea45b401ffee8df3957d2447d4ce80c83c5ff151fc6bfe1c4148
-  md5: d7e08fcf8259d742156188e8762b4d20
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 84237
-  timestamp: 1641347062780
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h59595ed_0.conda
-  sha256: a65bb5284369e548a15a44b14baf1f7ac34fa4718d7d987dd29032caba2ecf20
-  md5: 965eaacd7c18eb8361fd12bb9e7a57d7
+  - libgcc >=14
+  - __glibc >=2.17,<3.0.a0
+  license: MIT
+  license_family: MIT
+  size: 85189
+  timestamp: 1753484064210
+- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h4132b18_3.conda
+  sha256: a335161bfa57b64e6794c3c354e7d49449b28b8d8a7c4ed02bf04c3f009953f9
+  md5: a645bb90997d3fc2aea0adf6517059bd
   depends:
-  - libgcc-ng >=12
-  - libstdcxx-ng >=12
+  - __osx >=10.13
   license: MIT
   license_family: MIT
-  purls: []
-  size: 204867
-  timestamp: 1695710312002
-- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-he965462_0.conda
-  sha256: 6e5e4afa1011a1ad5a734e895b8d2b2ad0fbc9ef6538aac8f852b33b2ebe44a8
-  md5: 1bb3addc859ed1338370da6e2996ef47
+  size: 79419
+  timestamp: 1753484072608
+- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h3f2d84a_0.conda
+  sha256: 4b0b713a4308864a59d5f0b66ac61b7960151c8022511cdc914c0c0458375eca
+  md5: 92b90f5f7a322e74468bb4909c7354b5
   depends:
-  - libcxx >=15.0.7
+  - libstdcxx >=13
+  - libgcc >=13
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
   license: MIT
   license_family: MIT
-  purls: []
-  size: 130328
-  timestamp: 1695710502498
-- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.5.4-pyha770c72_0.conda
-  sha256: 772972b3e2ebeeb6dd2a3209b95c99b23d21c6657ebf2f758f9e63ccfa28dfc8
-  md5: f4d2f4a372be452baebf8dbdcd9892ed
+  size: 223526
+  timestamp: 1745307989800
+- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-h92383a6_0.conda
+  sha256: 67d25c3aa2b4ee54abc53060188542d6086b377878ebf3e2b262ae7379e05a6d
+  md5: e15e9855092a8bdaaaed6ad5c173fffa
+  depends:
+  - libcxx >=18
+  - __osx >=10.13
+  license: MIT
+  license_family: MIT
+  size: 145204
+  timestamp: 1745308032698
+- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.8.1-pyha770c72_0.conda
+  sha256: 439ebef131ef2e4711f286375240f8d779fce2fe54b4ec786fb58c6c9141b17b
+  md5: 55a52c71e7919a4951cfc6cccf4fa16f
   depends:
   - dpath
   - plac
@@ -3659,74 +3534,54 @@ packages:
   - pyyaml
   license: MIT
   license_family: MIT
-  purls:
-  - pkg:pypi/yte?source=hash-mapping
-  size: 14311
-  timestamp: 1702295254855
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_0.conda
-  sha256: 232a30e4b0045c9de5e168dda0328dc0e28df9439cdecdfb97dd79c1c82c4cec
-  md5: fee389bf8a4843bd7a2248ce11b7f188
-  depends:
-  - python >=3.8
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/zipp?source=hash-mapping
-  size: 21702
-  timestamp: 1731262194278
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312hef9b889_1.conda
-  sha256: b97015e146437283f2213ff0e95abdc8e2480150634d81fbae6b96ee09f5e50b
-  md5: 8b7069e9792ee4e5b4919a7a306d2e67
+  size: 15805
+  timestamp: 1749657286268
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_1.conda
+  sha256: c2bcb8aa930d6ea3c9c7a64fc4fab58ad7bcac483a9a45de294f67d2f447f413
+  md5: 02738ff9855946075cbd1b5274399a41
   depends:
-  - __glibc >=2.17,<3.0.a0
+  - python
   - cffi >=1.11
-  - libgcc >=13
-  - python >=3.12,<3.13.0a0
+  - zstd >=1.5.7,<1.5.8.0a0
+  - libgcc >=14
+  - __glibc >=2.17,<3.0.a0
+  - zstd >=1.5.7,<1.6.0a0
   - python_abi 3.12.* *_cp312
-  - zstd >=1.5.6,<1.5.7.0a0
-  - zstd >=1.5.6,<1.6.0a0
   license: BSD-3-Clause
-  license_family: BSD
-  purls:
-  - pkg:pypi/zstandard?source=hash-mapping
-  size: 419552
-  timestamp: 1725305670210
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py312h7122b0e_1.conda
-  sha256: 2685dde42478fae0780fba5d1f8a06896a676ae105f215d32c9f9e76f3c6d8fd
-  md5: bd132ba98f3fc0a6067f355f8efe4cb6
+  size: 467133
+  timestamp: 1762512686069
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.25.0-py312h01f6755_1.conda
+  sha256: 5360439241921c612a5df77e28ce0ae4912eef7de65dc42adba5499878a67e87
+  md5: d9209ec6445f95fba0c3c64fa4a46216
   depends:
-  - __osx >=10.13
+  - python
   - cffi >=1.11
-  - python >=3.12,<3.13.0a0
+  - zstd >=1.5.7,<1.5.8.0a0
+  - __osx >=10.13
   - python_abi 3.12.* *_cp312
-  - zstd >=1.5.6,<1.5.7.0a0
-  - zstd >=1.5.6,<1.6.0a0
+  - zstd >=1.5.7,<1.6.0a0
   license: BSD-3-Clause
-  license_family: BSD
-  purls:
-  - pkg:pypi/zstandard?source=hash-mapping
-  size: 410873
-  timestamp: 1725305688706
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
-  sha256: c558b9cc01d9c1444031bd1ce4b9cff86f9085765f17627a6cd85fc623c8a02b
-  md5: 4d056880988120e29d75bfff282e0f45
+  size: 462661
+  timestamp: 1762512711429
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
+  sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
+  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
   depends:
-  - libgcc-ng >=12
-  - libstdcxx-ng >=12
-  - libzlib >=1.2.13,<2.0.0a0
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
   license: BSD-3-Clause
   license_family: BSD
-  purls: []
-  size: 554846
-  timestamp: 1714722996770
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
-  sha256: efa04a98cb149643fa54c4dad5a0179e36a5fbc88427ea0eec88ceed87fd0f96
-  md5: 4cb2cd56f039b129bb0e491c1164167e
+  size: 567578
+  timestamp: 1742433379869
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.7-h8210216_2.conda
+  sha256: c171c43d0c47eed45085112cb00c8c7d4f0caa5a32d47f2daca727e45fb98dca
+  md5: cd60a4a5a8d6a476b30d8aa4bb49251a
   depends:
-  - __osx >=10.9
-  - libzlib >=1.2.13,<2.0.0a0
+  - __osx >=10.13
+  - libzlib >=1.3.1,<2.0a0
   license: BSD-3-Clause
   license_family: BSD
-  purls: []
-  size: 498900
-  timestamp: 1714723303098
+  size: 485754
+  timestamp: 1742433356230

From ff517469a7ae607fe5291a02846c03e58c698b88 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 16 Jun 2026 14:40:21 +0000
Subject: [PATCH 08/17] fix: rename [workspace] to [project] in pixi.toml for
 pixi v0.37.0 compatibility

---
 pixi.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index 6ae4ccb51..47acb066f 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,4 +1,4 @@
-[workspace]
+[project]
 authors = ["Mitchell Robert Vollger <mrvollger@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 description = "Add a short description here"

From 545ca74f08d3179db16806ce44b198ce5b6dfbc9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 16 Jun 2026 14:43:37 +0000
Subject: [PATCH 09/17] fix: update pixi version to v0.70.2 in CI, revert
 [workspace] in pixi.toml

---
 .github/workflows/main.yml | 2 +-
 pixi.toml                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8af20c95b..01e869b86 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -14,6 +14,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.37.0
+          pixi-version: v0.70.2
           cache: true
       - run: pixi run test
diff --git a/pixi.toml b/pixi.toml
index 47acb066f..6ae4ccb51 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,4 +1,4 @@
-[project]
+[workspace]
 authors = ["Mitchell Robert Vollger <mrvollger@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 description = "Add a short description here"

From 037d362f50f3cc93454c15abac4cf7e89c0a323c Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Tue, 16 Jun 2026 09:06:16 -0600
Subject: [PATCH 10/17] update

---
 pixi.toml                               | 70 ++++++++++++-------------
 workflow/Snakefile                      |  6 ++-
 workflow/rules/fire-peaks.smk           |  4 ++
 workflow/scripts/cov.py                 |  4 ++
 workflow/scripts/percent-in-clusters.py |  4 +-
 5 files changed, 49 insertions(+), 39 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index 6ae4ccb51..cd59a75eb 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -9,48 +9,48 @@ version = "0.1.2"
 [tasks]
 fmt = "ruff format . && taplo format pixi.toml && snakefmt workflow/"
 test-data = { cmd = [
-    "cd",
-    "$INIT_CWD",
-    "&&",
-    "mkdir",
-    "-p",
-    "fire-test-data",
-    "&&",
-    "rclone",
-    "sync",
-    ":s3,env_auth=false,provider=Other,endpoint=s3.kopah.orci.washington.edu:stergachis/public/FIRE/test-data",
-    "fire-test-data/",
+  "cd",
+  "$INIT_CWD",
+  "&&",
+  "mkdir",
+  "-p",
+  "fire-test-data",
+  "&&",
+  "rclone",
+  "sync",
+  ":s3,env_auth=false,provider=Other,endpoint=s3.kopah.orci.washington.edu:stergachis/public/FIRE/test-data",
+  "fire-test-data/",
 ] }
 test = { cmd = [
-    "cd",
-    "$INIT_CWD/fire-test-data",
-    "&&",
-    "snakemake",
-    "-s",
-    "$PIXI_PROJECT_ROOT/workflow/Snakefile",
-    "--configfile",
-    "test.yaml",
-    "-k",
+  "cd",
+  "$INIT_CWD/fire-test-data",
+  "&&",
+  "snakemake",
+  "-s",
+  "$PIXI_PROJECT_ROOT/workflow/Snakefile",
+  "--configfile",
+  "test.yaml",
+  "-k",
 ], depends-on = [
-    "test-data",
+  "test-data",
 ], clean-env = true }
 fire = { cmd = [
-    "cd",
-    "$INIT_CWD",
-    "&&",
-    "snakemake",
-    "-s",
-    "$PIXI_PROJECT_ROOT/workflow/Snakefile",
+  "cd",
+  "$INIT_CWD",
+  "&&",
+  "snakemake",
+  "-s",
+  "$PIXI_PROJECT_ROOT/workflow/Snakefile",
 ] }
 slurm = { cmd = [
-    "cd",
-    "$INIT_CWD",
-    "&&",
-    "snakemake",
-    "-s",
-    "$PIXI_PROJECT_ROOT/workflow/Snakefile",
-    "--profile",
-    "$PIXI_PROJECT_ROOT/profiles/slurm-executor",
+  "cd",
+  "$INIT_CWD",
+  "&&",
+  "snakemake",
+  "-s",
+  "$PIXI_PROJECT_ROOT/workflow/Snakefile",
+  "--profile",
+  "$PIXI_PROJECT_ROOT/profiles/slurm-executor",
 ] }
 
 [dependencies]
diff --git a/workflow/Snakefile b/workflow/Snakefile
index d8b132cf1..dc1e50fdb 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -23,7 +23,7 @@ FULL_VERSION = f"v{os.environ.get("PIXI_PROJECT_VERSION", "UNK")}"
 # trim the FULL_VERSION to just the just the major and minor version
 VERSION = ".".join(FULL_VERSION.split(".")[:2])
 
-# use the full version if requested 
+# use the full version if requested
 if config.get("full-version", False):
     VERSION = FULL_VERSION
 
@@ -130,7 +130,9 @@ rule all:
         # coverage information
         expand(rules.coverage.output, sm=MANIFEST.index, v=VERSION),
         expand(rules.exclude_from_shuffle.output, sm=MANIFEST.index, v=VERSION),
-        expand(rules.unreliable_coverage_regions.output.bed, sm=MANIFEST.index, v=VERSION),
+        expand(
+            rules.unreliable_coverage_regions.output.bed, sm=MANIFEST.index, v=VERSION
+        ),
         # model results
         expand(rules.fire.output.cram, sm=MANIFEST.index, v=VERSION),
         expand(rules.fire_sites.output, sm=MANIFEST.index, v=VERSION),
diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk
index c4471427a..dbaf99c31 100644
--- a/workflow/rules/fire-peaks.smk
+++ b/workflow/rules/fire-peaks.smk
@@ -76,10 +76,12 @@ rule fdr_table:
         "../envs/python.yaml"
     params:
         script=workflow.source_path("../scripts/fdr-table.py"),
+    threads: 16
     resources:
         mem_mb=get_mem_mb_xl,
     shell:
         """
+        export POLARS_MAX_THREADS={threads}
         MIN=$(cat {input.minimum})
         MAX=$(cat {input.maximum})
         python {params.script} -v 1 {input.shuffled} {output.tbl} --max-cov $MAX --min-cov $MIN
@@ -124,6 +126,7 @@ rule fdr_track_chromosome:
         mem_mb=get_mem_mb_xl,
     shell:
         """
+        export POLARS_MAX_THREADS={threads}
         python {params.script} -v 1 \
             --fdr-table {input.fdr_tbl} \
             {input.pileup} {output.bed}
@@ -231,6 +234,7 @@ rule fdr_peaks_by_fire_elements_chromosome:
         min_frac_accessible=MIN_FRAC_ACCESSIBLE,
     shell:
         """
+        export POLARS_MAX_THREADS={threads}
         bgzip -cd {input.bed} \
             | python {params.script} -v 1 \
                 --max-cov $(cat {input.maximum}) \
diff --git a/workflow/scripts/cov.py b/workflow/scripts/cov.py
index 0754ef914..53044ec13 100644
--- a/workflow/scripts/cov.py
+++ b/workflow/scripts/cov.py
@@ -1,3 +1,7 @@
+import os
+
+os.environ["POLARS_MAX_THREADS"] = str(snakemake.threads)
+
 import pandas as pd
 import sys
 import math
diff --git a/workflow/scripts/percent-in-clusters.py b/workflow/scripts/percent-in-clusters.py
index 4a86c3595..e0ae7437b 100644
--- a/workflow/scripts/percent-in-clusters.py
+++ b/workflow/scripts/percent-in-clusters.py
@@ -16,7 +16,7 @@ def my_groupby(gdf):
 real_bp = (df[df.case == "Real"]["length"] * df[df.case == "Real"]["cov"]).sum()
 df = df.groupby("cov").apply(my_groupby).reset_index()
 over_expected = df[0][df[0] > 0].sum()
-print(f"{over_expected/real_bp:%}\n")
+print(f"{over_expected / real_bp:%}\n")
 
 # chr1    0       1       12      1       1       1
 cov = sys.argv[2]
@@ -28,7 +28,7 @@ def my_groupby(gdf):
 
 
 rtn = f"""percent-of-MSPs-preferentially-clustered-along-the-genome\tmin_fdr
-{over_expected/real_bp:%}\t{min_fdr}
+{over_expected / real_bp:%}\t{min_fdr}
 """
 out = sys.argv[3]
 open(out, "w").write(rtn)

From 782c21bf36b9878be9476441f20428f4d3dba6e2 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 07:15:06 -0700
Subject: [PATCH 11/17] update fibertools-rs to 0.12.0

ft pileup no longer takes the region as a positional argument, so pass
it via --rgn. samtools/htslib 1.21 and bedtools 2.31.1 are required to
get builds compatible with the libzlib>=1.3.2 that ft 0.12 links.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 workflow/envs/env.yaml        | 8 ++++----
 workflow/rules/fire-peaks.smk | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/workflow/envs/env.yaml b/workflow/envs/env.yaml
index 07984df4c..7b137dc05 100644
--- a/workflow/envs/env.yaml
+++ b/workflow/envs/env.yaml
@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - samtools==1.19.1
-  - htslib==1.19.1
-  - bedtools==2.31
-  - bioconda::fibertools-rs==0.6
+  - samtools==1.21
+  - htslib==1.21
+  - bedtools==2.31.1
+  - bioconda::fibertools-rs==0.12.0
   - hck>=0.9.2
   - bioawk
   - ripgrep
diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk
index dbaf99c31..cbf5a9f0a 100644
--- a/workflow/rules/fire-peaks.smk
+++ b/workflow/rules/fire-peaks.smk
@@ -34,7 +34,7 @@ rule shuffled_pileup_chromosome:
         DEFAULT_ENV
     shell:
         """
-        {FT_EXE} pileup {input.cram} {wildcards.chrom} -t {threads} \
+        {FT_EXE} pileup {input.cram} --rgn {wildcards.chrom} -t {threads} \
             --fiber-coverage --shuffle {input.shuffled} \
             --no-msp --no-nuc \
             | bgzip -@ {threads} \
@@ -105,7 +105,7 @@ rule pileup_chromosome:
         """
         {FT_EXE} pileup -t {threads} \
             --haps --fiber-coverage \
-            {input.bam} {wildcards.chrom} \
+            {input.bam} --rgn {wildcards.chrom} \
             | bgzip -@ {threads} \
             > {output.bed}
         """

From 5214ea88dfc15f16411b0f965be06614be5cc305 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 09:48:42 -0700
Subject: [PATCH 12/17] Port PR #55 leftovers and v0.2.0 housekeeping

- exclude_from_shuffle: guard empty EXCLUDES (non-hg38 refs) and use
  gunzip -cf instead of less for portable plain/gzip handling
- pixi: skip test-data download when already present, add test-clean,
  start test runs from a clean state, fill in description, bump to 0.2.0
- CI: setup-pixi action v0.8.1 -> v0.9.6
- CHANGELOG for v0.2.0; ruff formatting in two scripts

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 .github/workflows/main.yml           |  2 +-
 CHANGELOG.md                         |  9 ++++++++
 pixi.toml                            | 31 +++++-----------------------
 workflow/rules/coverages.smk         | 11 +++++-----
 workflow/scripts/fdr-table.py        |  2 +-
 workflow/scripts/merge_fire_peaks.py |  7 ++++++-
 6 files changed, 28 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 01e869b86..037f5d4e8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: prefix-dev/setup-pixi@v0.8.1
+      - uses: prefix-dev/setup-pixi@v0.9.6
         with:
           pixi-version: v0.70.2
           cache: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5769cd383..653e3e817 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,15 @@
 
 All notable changes to this project will be documented in this file.
 
+## v0.2.0
+
+- Update fibertools-rs to 0.12.x (requires `ft pileup --rgn`; also updates samtools,
+  htslib, and bedtools pins in `workflow/envs/env.yaml`)
+- Polars fixes: explicit schemas for chrom/score columns (#48, #52, #53, #56)
+- `exclude_from_shuffle` now works when no `excludes` are configured (non-hg38 refs)
+- Test data now downloaded via rclone; test runs start from a clean state
+  (`test-clean` task added)
+
 ## v0.1.2
 
 - fix #34
diff --git a/pixi.toml b/pixi.toml
index cd59a75eb..dc98c8410 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,37 +1,16 @@
 [workspace]
 authors = ["Mitchell Robert Vollger <mrvollger@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
-description = "Add a short description here"
+description = "A Snakemake pipeline for calling FIRE peaks using fibertools-rs."
 name = "FIRE"
 platforms = ["osx-64", "linux-64"]
-version = "0.1.2"
+version = "0.2.0"
 
 [tasks]
 fmt = "ruff format . && taplo format pixi.toml && snakefmt workflow/"
-test-data = { cmd = [
-  "cd",
-  "$INIT_CWD",
-  "&&",
-  "mkdir",
-  "-p",
-  "fire-test-data",
-  "&&",
-  "rclone",
-  "sync",
-  ":s3,env_auth=false,provider=Other,endpoint=s3.kopah.orci.washington.edu:stergachis/public/FIRE/test-data",
-  "fire-test-data/",
-] }
-test = { cmd = [
-  "cd",
-  "$INIT_CWD/fire-test-data",
-  "&&",
-  "snakemake",
-  "-s",
-  "$PIXI_PROJECT_ROOT/workflow/Snakefile",
-  "--configfile",
-  "test.yaml",
-  "-k",
-], depends-on = [
+test-data = { cmd = '''bash -c 'if [ -f "$INIT_CWD/fire-test-data/test.cram" ]; then echo "test data already present, skipping download"; else mkdir -p "$INIT_CWD/fire-test-data" && rclone sync ":s3,env_auth=false,provider=Other,endpoint=s3.kopah.orci.washington.edu:stergachis/public/FIRE/test-data" "$INIT_CWD/fire-test-data/"; fi' ''' }
+test-clean = { cmd = '''bash -c 'cd "$INIT_CWD/fire-test-data" && rm -rf results temp .snakemake' ''' }
+test = { cmd = '''bash -c 'cd "$INIT_CWD/fire-test-data" && rm -rf results temp && snakemake -s "$PIXI_PROJECT_ROOT/workflow/Snakefile" --configfile test.yaml -k' ''', depends-on = [
   "test-data",
 ], clean-env = true }
 fire = { cmd = [
diff --git a/workflow/rules/coverages.smk b/workflow/rules/coverages.smk
index 9a0aa1394..e7eb5ea89 100644
--- a/workflow/rules/coverages.smk
+++ b/workflow/rules/coverages.smk
@@ -126,13 +126,14 @@ rule exclude_from_shuffle:
     conda:
         DEFAULT_ENV
     params:
-        exclude=EXCLUDES,
+        exclude=lambda wc: " ".join(EXCLUDES) if EXCLUDES else "",
     shell:
         """
-
-        ( \
-            bedtools genomecov -bga -i {input.filtered} -g {input.fai} | awk '$4 == 0'; \
-            less {params.exclude} \
+        (
+            bedtools genomecov -bga -i {input.filtered} -g {input.fai} | awk '$4 == 0'
+            if [ -n "{params.exclude}" ]; then
+                gunzip -cf {params.exclude}
+            fi
         ) \
             | cut -f 1-3 \
             | bedtools sort \
diff --git a/workflow/scripts/fdr-table.py b/workflow/scripts/fdr-table.py
index 3c185ead3..aa4f3505a 100644
--- a/workflow/scripts/fdr-table.py
+++ b/workflow/scripts/fdr-table.py
@@ -59,7 +59,7 @@ def read_pileup_file(infile, nrows):
     # add scema overrides for the score columns
     # Build schema overrides keyed by positional column names (column_1, column_2, ...)
     # because polars infers schema BEFORE new_columns is applied when has_header=False.
-    # Keying on '#chrom' / 'score' here would be silently ignored. 
+    # Keying on '#chrom' / 'score' here would be silently ignored.
     schema_overrides = {}
     for col_idx, col_name in enumerate(header, start=1):
         positional = f"column_{col_idx}"
diff --git a/workflow/scripts/merge_fire_peaks.py b/workflow/scripts/merge_fire_peaks.py
index 8867cec37..71d84ce29 100755
--- a/workflow/scripts/merge_fire_peaks.py
+++ b/workflow/scripts/merge_fire_peaks.py
@@ -124,7 +124,12 @@ def main(
     logger.setLevel(log_level)
 
     inf = io.StringIO(sys.stdin.read())
-    df = pl.read_csv(inf, separator="\t", null_values=".", schema_overrides={"#chrom": pl.Utf8},)
+    df = pl.read_csv(
+        inf,
+        separator="\t",
+        null_values=".",
+        schema_overrides={"#chrom": pl.Utf8},
+    )
     if df.shape[0] == 0:
         logging.info("No peaks to merge")
         return 0

From 045a60e65f9d552299084875f6e817b901cc28de Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 09:58:26 -0700
Subject: [PATCH 13/17] 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 <noreply@anthropic.com>
---
 CHANGELOG.md       | 3 +++
 config/README.md   | 4 ++--
 workflow/Snakefile | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 653e3e817..aae1013cb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 
 ## v0.2.0
 
+- `min_frac_accessible` now defaults to 0.10: FIRE peaks must have at least 10%
+  of reads accessible in addition to passing FDR peak calling (set to 0.0 to
+  restore the old behavior)
 - Update fibertools-rs to 0.12.x (requires `ft pileup --rgn`; also updates samtools,
   htslib, and bedtools pins in `workflow/envs/env.yaml`)
 - Polars fixes: explicit schemas for chrom/score columns (#48, #52, #53, #56)
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

From 157e981c98a57fb903876f0c843cd01feae48753 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 10:02:56 -0700
Subject: [PATCH 14/17] Pin fibertools-rs >=0.13,<0.14

0.12.0 has a bug where ft fire --extract reports FDR=1.0 for every MSP
(fixed upstream in fibertools-rs#121); wait for the 0.13 release rather
than 0.12.1.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 workflow/envs/env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/envs/env.yaml b/workflow/envs/env.yaml
index 7b137dc05..bc938e0cc 100644
--- a/workflow/envs/env.yaml
+++ b/workflow/envs/env.yaml
@@ -7,7 +7,7 @@ dependencies:
   - samtools==1.21
   - htslib==1.21
   - bedtools==2.31.1
-  - bioconda::fibertools-rs==0.12.0
+  - bioconda::fibertools-rs>=0.13,<0.14
   - hck>=0.9.2
   - bioawk
   - ripgrep

From d77b331ef2279f9317d4f2dcc24cd98f70997969 Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 17:09:26 -0700
Subject: [PATCH 15/17] Note fibertools-rs 0.13.x in changelog

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aae1013cb..f87e1cb6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ All notable changes to this project will be documented in this file.
 - `min_frac_accessible` now defaults to 0.10: FIRE peaks must have at least 10%
   of reads accessible in addition to passing FDR peak calling (set to 0.0 to
   restore the old behavior)
-- Update fibertools-rs to 0.12.x (requires `ft pileup --rgn`; also updates samtools,
+- Update fibertools-rs to 0.13.x (requires `ft pileup --rgn`; also updates samtools,
   htslib, and bedtools pins in `workflow/envs/env.yaml`)
 - Polars fixes: explicit schemas for chrom/score columns (#48, #52, #53, #56)
 - `exclude_from_shuffle` now works when no `excludes` are configured (non-hg38 refs)

From 89ed5a75bed9c89833c8778d1d5bcbf52940e2ec Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 17:19:20 -0700
Subject: [PATCH 16/17] Switch mac support from Intel (osx-64) to Apple Silicon
 (osx-arm64)

bioconda no longer ships osx-64 builds of fibertools-rs (0.13.0 is
linux-64/osx-arm64 only). Bump samtools/htslib to 1.24, mosdepth to
0.3.14, and bigtools to 0.5.8 for osx-arm64 availability and libdeflate
compatibility; python env htslib to 1.20 (oldest with an arm build).
All four workflow envs and the pixi env solve on both osx-arm64 and
linux-64.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 CHANGELOG.md              |    3 +
 pixi.lock                 | 2634 +++++++++++++++++++++++++++----------
 pixi.toml                 |    2 +-
 workflow/envs/env.yaml    |    8 +-
 workflow/envs/python.yaml |    2 +-
 5 files changed, 1920 insertions(+), 729 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f87e1cb6b..6565a6854 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,9 @@ All notable changes to this project will be documented in this file.
 - `exclude_from_shuffle` now works when no `excludes` are configured (non-hg38 refs)
 - Test data now downloaded via rclone; test runs start from a clean state
   (`test-clean` task added)
+- Mac support moved from Intel (osx-64) to Apple Silicon (osx-arm64), following
+  bioconda's fibertools-rs builds; samtools/htslib 1.24, mosdepth 0.3.14,
+  bigtools 0.5.8
 
 ## v0.1.2
 
diff --git a/pixi.lock b/pixi.lock
index f74a90fde..060ac2f1c 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -191,181 +191,214 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.8.1-pyha770c72_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
-      osx-64:
-      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+      osx-arm64:
+      - conda: https://conda.anaconda.org/conda-forge/osx-arm64/_openmp_mutex-4.5-7_kmp_llvm.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.7-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-doc-0.0.5-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.8.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.14.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyhd8ed1ab_1.conda
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda
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-  - libzlib >=1.3.1,<2.0a0
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/coin-or-cgl-0.60.9-hbb40df2_6.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/coin-or-clp-1.17.10-heb008f4_3.conda
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   - libcxx >=19
   - libgfortran
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-  - libgfortran5 >=15.2.0
   - liblapack >=3.9.0,<4.0a0
-  - libzlib >=1.3.1,<2.0a0
+  - libzlib >=1.3.2,<2.0a0
   constrains:
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   license: EPL-2.0
   license_family: OTHER
-  size: 631867
-  timestamp: 1762926692851
+  size: 553075
+  timestamp: 1778500827484
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/conda-25.9.1-py312hb401068_0.conda
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   - packaging >=23.0
   - platformdirs >=3.10.0
-  - pluggy >=1.0.0
+  - pluggy >=1.6.0
   - pycosat >=0.6.3
-  - python >=3.12,<3.13.0a0
-  - python_abi 3.12.* *_cp312
+  - python
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   - ruamel.yaml >=0.11.14,<0.19
   - setuptools >=60.0.0
   - tqdm >=4
   - truststore >=0.8.0
-  - zstandard >=0.19.0
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+  - conda-pypi >=0.10.1
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+  - conda-self >=0.2.0
+  - python 3.12.* *_cpython
+  - python_abi 3.12.* *_cp312
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   - conda-build >=25.9
+  - conda-content-trust >=0.3.0
   - conda-env >=2.6
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   license_family: BSD
-  size: 1208983
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+  - filelock
+  - jinja2
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+  - python >=3.10
+  - ruamel.yaml
+  - zstandard
+  license: BSD-3-Clause
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   timestamp: 1745834587643
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@@ -954,6 +1191,19 @@ packages:
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   timestamp: 1736345601691
+- conda: https://conda.anaconda.org/conda-forge/noarch/conda-package-handling-2.5.0-pyhcf101f3_0.conda
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 - conda: https://conda.anaconda.org/conda-forge/noarch/conda-package-streaming-0.12.0-pyhd8ed1ab_0.conda
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@@ -964,6 +1214,59 @@ packages:
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+  - python_abi 3.12.* *_cp312
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@@ -974,6 +1277,17 @@ packages:
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   size: 40511
   timestamp: 1748302135421
+- conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7.5-pyhcf101f3_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/cpp-expected-1.3.1-h0ba0a54_0.conda
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   - libcxx >=19
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+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.12.13-py312hd8ed1ab_1.conda
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+  - python_abi * *_cp312
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/datrie-0.8.3-py312h2f459f6_0.conda
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   - python_abi 3.12.* *_cp312
   license: LGPL-2.1-or-later
   license_family: LGPL
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   size: 436965
   timestamp: 1762425841874
+- conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.23-pyhcf101f3_0.conda
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@@ -1064,6 +1399,19 @@ packages:
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+- conda: https://conda.anaconda.org/conda-forge/noarch/eido-0.2.6-pyhd8ed1ab_0.conda
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   timestamp: 1746947398083
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+  - python >=3.10
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   timestamp: 1753444241693
+- conda: https://conda.anaconda.org/conda-forge/noarch/gitpython-3.1.59-pyhcf101f3_0.conda
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   size: 95967
   timestamp: 1756364871835
+- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.4.1-pyhcf101f3_0.conda
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+  - python
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   size: 30731
   timestamp: 1737618390337
+- conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.2.0-pyhd8ed1ab_0.conda
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+  - h11 >=0.16
+  - h2 >=3,<5
+  - sniffio 1.*
+  - anyio >=4.0,<5.0
+  - certifi
+  - python
+  license: BSD-3-Clause
+  license_family: BSD
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+- conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.28.1-pyhd8ed1ab_0.conda
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+  - python >=3.9
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 - conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda
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@@ -1189,6 +1632,15 @@ packages:
   license_family: MIT
   size: 12129203
   timestamp: 1720853576813
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/icu-78.3-py310h579977c_2.conda
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 - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
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@@ -1198,6 +1650,16 @@ packages:
   license_family: BSD
   size: 50721
   timestamp: 1760286526795
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.18-pyhcf101f3_0.conda
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+  - python
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/immutables-0.21-py312h4c3975b_2.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/immutables-0.21-py312h2f459f6_2.conda
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-  md5: 5baa48efc6d041e4033402f8797ea18b
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+  - __osx >=11.0
   - python >=3.12,<3.13.0a0
+  - python >=3.12,<3.13.0a0 *_cpython
   - python_abi 3.12.* *_cp312
   license: Apache-2.0
   license_family: APACHE
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+  - zipp >=3.20
+  - python
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@@ -1230,6 +1704,17 @@ packages:
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   timestamp: 1760831448842
+- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
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+  - python >=3.10
+  - python
+  license: BSD-3-Clause
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 - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhd8ed1ab_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/jsonpointer-3.0.0-py312hb401068_2.conda
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-  md5: 7632694baab67c90efad51eb38e53fbd
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonpointer-3.1.1-pyhcf101f3_0.conda
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+  md5: 89bf346df77603055d3c8fe5811691e6
   depends:
-  - python >=3.12,<3.13.0a0
-  - python_abi 3.12.* *_cp312
+  - python >=3.10
+  - python
   license: BSD-3-Clause
   license_family: BSD
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@@ -1284,6 +1769,20 @@ packages:
   license_family: MIT
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   timestamp: 1755595646123
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
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+  md5: ada41c863af263cc4c5fcbaff7c3e4dc
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+  - jsonschema-specifications >=2023.3.6
+  - python >=3.10
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+  - rpds-py >=0.25.0
+  - python
+  license: MIT
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 - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/krb5-1.21.3-h37d8d59_0.conda
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-  - libedit >=3.1.20191231,<4.0a0
-  - openssl >=3.3.1,<4.0a0
+  - __osx >=11.0
+  - libcxx >=19
+  - libedit >=3.1.20250104,<3.2.0a0
+  - libedit >=3.1.20250104,<4.0a0
+  - openssl >=3.5.7,<4.0a0
   license: MIT
   license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libarchive-3.8.2-gpl_h889603c_100.conda
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+  - __osx >=11.0
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   - libiconv >=1.18,<2.0a0
-  - liblzma >=5.8.1,<6.0a0
+  - liblzma >=5.8.3,<6.0a0
   - libxml2
   - libxml2-16 >=2.14.6
-  - libzlib >=1.3.1,<2.0a0
+  - libzlib >=1.3.2,<2.0a0
   - lz4-c >=1.10.0,<1.11.0a0
   - lzo >=2.10,<3.0a0
-  - openssl >=3.5.4,<4.0a0
+  - openssl >=3.5.7,<4.0a0
   - zstd >=1.5.7,<1.6.0a0
   license: BSD-2-Clause
   license_family: BSD
-  size: 760450
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-38_he492b99_openblas.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libblas-3.11.0-9_h51639a9_openblas.conda
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-  - blas 2.138   openblas
-  - liblapack  3.9.0   38*_openblas
-  - liblapacke 3.9.0   38*_openblas
+  - blas 2.309   openblas
+  - libcblas   3.11.0   9*_openblas
+  - liblapack  3.11.0   9*_openblas
+  - liblapacke 3.11.0   9*_openblas
+  - mkl <2027
   license: BSD-3-Clause
   license_family: BSD
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-38_h0358290_openblas.conda
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@@ -1444,20 +1943,20 @@ packages:
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libcblas-3.9.0-38_h9b27e0a_openblas.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libcblas-3.11.0-9_hb0561ab_openblas.conda
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+  md5: a7b6ba94e3ca58bc7d4e1ae4ff95c215
   depends:
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+  - libblas 3.11.0 9_h51639a9_openblas
   constrains:
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-  - liblapack  3.9.0   38*_openblas
-  - liblapacke 3.9.0   38*_openblas
+  - blas 2.309   openblas
+  - liblapack  3.11.0   9*_openblas
+  - liblapacke 3.11.0   9*_openblas
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   license_family: BSD
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libcurl-8.17.0-h7dd4100_0.conda
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   - libssh2 >=1.11.1,<2.0a0
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   license: curl
   license_family: MIT
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   depends:
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+  - __osx >=11.0
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libedit-3.1.20250104-pl5321ha958ccf_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libedit-3.1.20250104-pl5321h26f1114_1.conda
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-  - __osx >=10.13
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   license_family: BSD
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libev-4.33-h1a92334_3.conda
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+  - __osx >=11.0
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+  - expat 2.8.1.*
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   license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libffi-3.5.2-h750e83c_0.conda
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@@ -1592,6 +2094,18 @@ packages:
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   timestamp: 1759968052178
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libgcc-16.1.0-h3cf6597_1.conda
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+  md5: 0124dc2e6f70f3e8ebea643b42b18abb
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+  constrains:
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+  - libgcc-ng ==16.1.0=*_1
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 364162
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libgfortran-15.2.0-h306097a_1.conda
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+  - libgfortran5 16.1.0 h32cdfcc_1
+  constrains:
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   license: GPL-3.0-only WITH GCC-exception-3.1
   license_family: GPL
-  size: 134506
-  timestamp: 1759710031253
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libgfortran5-15.2.0-h336fb69_1.conda
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+  - libgcc >=16.1.0
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+  - libgfortran 16.1.0
   license: GPL-3.0-only WITH GCC-exception-3.1
   license_family: GPL
-  size: 1236316
-  timestamp: 1759709318982
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/liblapack-3.9.0-38_h859234e_openblas.conda
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-  md5: 062a7bd94939084574e2d401f8e0840e
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-  - libcblas   3.9.0   38*_openblas
-  - liblapacke 3.9.0   38*_openblas
+  - blas 2.309   openblas
+  - libcblas   3.11.0   9*_openblas
+  - liblapacke 3.11.0   9*_openblas
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   license_family: BSD
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-  timestamp: 1761680534375
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/liblapacke-3.9.0-38_h94b3770_openblas.conda
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-  - liblapack 3.9.0 38_h859234e_openblas
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/liblapacke-3.11.0-9_h1b118fd_openblas.conda
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+  - libcblas 3.11.0 9_hb0561ab_openblas
+  - liblapack 3.11.0 9_hd9741b5_openblas
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+  - blas 2.309   openblas
   license: BSD-3-Clause
   license_family: BSD
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   depends:
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+  - __osx >=11.0
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+  - xz 5.8.3.*
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libmamba-spdlog-2.9.0-heb3ad76_0.conda
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+  - __osx >=11.0
+  - libmamba >=2.9.0,<2.10.0a0
   license: BSD-3-Clause
   license_family: BSD
-  size: 1779068
-  timestamp: 1760729611665
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-- conda: https://conda.anaconda.org/conda-forge/osx-64/libmambapy-2.3.3-py312h1d4d8eb_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libmambapy-2.9.0-py312ha20c16a_0.conda
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-  - libmamba ==2.3.3 hf3f6d74_1
-  - __osx >=10.13
+  - libmamba ==2.9.0 py314hf3ae1d6_0
+  - libmamba-spdlog ==2.9.0 heb3ad76_0
   - libcxx >=19
-  - python_abi 3.12.* *_cp312
+  - __osx >=11.0
+  - python 3.12.* *_cpython
   - yaml-cpp >=0.8.0,<0.9.0a0
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-  - pybind11-abi ==4
-  - openssl >=3.5.4,<4.0a0
-  - nlohmann_json-abi ==3.12.0
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+  - python_abi 3.12.* *_cp312
+  - pybind11-abi ==11
+  - spdlog >=1.17.0,<1.18.0a0
   - zstd >=1.5.7,<1.6.0a0
+  - nlohmann_json-abi ==3.12.0
+  - libmamba >=2.9.0,<2.10.0a0
+  - openssl >=3.5.7,<4.0a0
   license: BSD-3-Clause
   license_family: BSD
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.67.0-had1ee68_0.conda
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   timestamp: 1756834976695
-- conda: https://conda.anaconda.org/conda-forge/osx-64/libnghttp2-1.67.0-h3338091_0.conda
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   license: MIT
   license_family: MIT
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   license: BSD-3-Clause
   license_family: BSD
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   license_family: BSD
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-  - libzlib >=1.3.1,<2.0a0
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+  - libxml2-16 2.15.3 h5ef1a60_0
+  - libzlib >=1.3.2,<2.0a0
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-  - libzlib >=1.3.1,<2.0a0
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   license: Zlib
   license_family: Other
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-  - openmp 21.1.5|21.1.5.*
+  - openmp 22.1.8|22.1.8.*
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   license_family: APACHE
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   timestamp: 1754951288511
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   license_family: BSD
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   size: 89498
   timestamp: 1735661472632
+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.70.0-pyh8f84b5b_0.conda
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+  depends:
+  - python >=3.10
+  - __unix
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+  - envwrap >=0.2
+  - ipywidgets >=6.0
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 - conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_1.conda
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@@ -3344,6 +4393,16 @@ packages:
   license_family: BSD
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   timestamp: 1733367480074
+- conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.16.1-pyhcf101f3_0.conda
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+  md5: a79bf97561232a31447b6246c2153ab5
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+  - python
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 - conda: https://conda.anaconda.org/conda-forge/noarch/truststore-0.10.3-pyhe01879c_0.conda
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@@ -3354,6 +4413,16 @@ packages:
   license_family: MIT
   size: 23801
   timestamp: 1753886790616
+- conda: https://conda.anaconda.org/conda-forge/noarch/truststore-0.10.4-pyhcf101f3_0.conda
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+  md5: c2db35b004913ec69bcac64fb0783de0
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+  - python
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.20.0-pyhdb1f59b_0.conda
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   md5: 27ec7c3f99366fa64228c3ee4ab49cbc
@@ -3365,6 +4434,19 @@ packages:
   license_family: MIT
   size: 79367
   timestamp: 1760982314002
+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.27.1-pyhcf101f3_0.conda
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+  - annotated-doc >=0.0.2
+  - colorama
+  - python >=3.10
+  - rich >=13.8.0
+  - shellingham >=1.3.0
+  - python
+  license: MIT AND BSD-3-Clause
+  size: 188113
+  timestamp: 1785796291853
 - conda: https://conda.anaconda.org/conda-forge/noarch/typer-slim-0.20.0-pyhcf101f3_0.conda
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@@ -3401,6 +4483,15 @@ packages:
   license_family: PSF
   size: 91383
   timestamp: 1756220668932
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.16.0-h69aa097_0.conda
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+  md5: c680b5747e8c4c8f23dca0bb7042a8fc
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+  timestamp: 1783002732887
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_0.conda
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   md5: 399701494e731ce73fdd86c185a3d1b4
@@ -3411,6 +4502,17 @@ packages:
   license_family: MIT
   size: 18799
   timestamp: 1759301271883
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.3-pyhcf101f3_0.conda
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+  md5: 4934c9f5695514b925be8a5503bcd171
+  depends:
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+  - typing_extensions >=4.15.0
+  - python
+  license: MIT
+  license_family: MIT
+  size: 20940
+  timestamp: 1786372593154
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
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   md5: 0caa1af407ecff61170c9437a808404d
@@ -3421,12 +4523,28 @@ packages:
   license_family: PSF
   size: 51692
   timestamp: 1756220668932
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.16.0-pyhcf101f3_0.conda
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+  - python >=3.10
+  - python
+  license: PSF-2.0
+  license_family: PSF
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+  timestamp: 1783002732887
 - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda
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   md5: 4222072737ccff51314b5ece9c7d6f5a
   license: LicenseRef-Public-Domain
   size: 122968
   timestamp: 1742727099393
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda
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+  license: LicenseRef-Public-Domain
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 - conda: https://conda.anaconda.org/conda-forge/noarch/ubiquerg-0.8.0-pyhd8ed1ab_0.conda
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@@ -3437,6 +4555,28 @@ packages:
   license_family: BSD
   size: 20698
   timestamp: 1719492750373
+- conda: https://conda.anaconda.org/conda-forge/noarch/ubiquerg-0.9.3-pyhd8ed1ab_0.conda
+  sha256: 33afef3f9b2e3b73254a9401cf7a101632ac74f704fdf7e744ca896720797caa
+  md5: 04429efde19509f6672b9f9434676ae9
+  depends:
+  - python >=3.10
+  license: BSD-2-Clause
+  license_family: BSD
+  size: 23293
+  timestamp: 1775148942723
+- conda: https://conda.anaconda.org/conda-forge/noarch/unearth-0.18.2-pyhd8ed1ab_0.conda
+  sha256: 2fe118c7c33571613cd12f7e9771049e19a46abaa6abfa4adc92d0defc54c61e
+  md5: a85b53859c40d115022948c8f225d8d6
+  depends:
+  - cached-property >=1.5.2
+  - httpx
+  - packaging >=20
+  - python >=3.10
+  - requests >=2.25
+  license: MIT
+  license_family: MIT
+  size: 286235
+  timestamp: 1766474788879
 - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.5.0-pyhd8ed1ab_0.conda
   sha256: 4fb9789154bd666ca74e428d973df81087a697dbb987775bc3198d2215f240f8
   md5: 436c165519e140cb08d246a4472a9d6a
@@ -3450,6 +4590,19 @@ packages:
   license_family: MIT
   size: 101735
   timestamp: 1750271478254
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
+  sha256: feff959a816f7988a0893201aa9727bbb7ee1e9cec2c4f0428269b489eb93fb4
+  md5: cbb88288f74dbe6ada1c6c7d0a97223e
+  depends:
+  - backports.zstd >=1.0.0
+  - brotli-python >=1.2.0
+  - h2 >=4,<5
+  - pysocks >=1.5.6,<2.0,!=1.5.7
+  - python >=3.10
+  license: MIT
+  license_family: MIT
+  size: 103560
+  timestamp: 1778188657149
 - conda: https://conda.anaconda.org/conda-forge/noarch/veracitools-0.1.3-py_0.tar.bz2
   sha256: f2222d612da9a362b8ff13c8411faa8077dff54fa2e71813c341aa0823b41b24
   md5: f2c8d44ea78cf639ab4810aedba43ab5
@@ -3460,6 +4613,16 @@ packages:
   license_family: BSD
   size: 6108
   timestamp: 1572717780817
+- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.48.0-pyhd8ed1ab_0.conda
+  sha256: ba64b29b6d418024cb565081a1799262cb2780d2534ff4c14f76aa858c4286cd
+  md5: 9a2124517bfd5d792e0f7b86eefdfeb8
+  depends:
+  - packaging >=24.0
+  - python >=3.10
+  license: MIT
+  license_family: MIT
+  size: 34528
+  timestamp: 1786613220176
 - conda: https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.17.3-py312h4c3975b_1.conda
   sha256: 8320d5af37eb8933e5d129884ea013b2687e75b08aff5216193df3378eaea92f
   md5: 8af3faf88325836e46c6cb79828e058c
@@ -3472,17 +4635,18 @@ packages:
   license_family: BSD
   size: 64608
   timestamp: 1756851740646
-- conda: https://conda.anaconda.org/conda-forge/osx-64/wrapt-1.17.3-py312h2f459f6_1.conda
-  sha256: df1430736e2b8ecfb559b7240478517c71d85697dee753628ef9ead84c3d1e52
-  md5: a92e23c22f481e7c8bc5d2dc551c101d
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/wrapt-1.17.3-py312h163523d_1.conda
+  sha256: b2be8bbfc1d7d63cd82f23c6aab0845b5dbbd835378b3c4e61b80b7d81ae9656
+  md5: 5658c0733acef1e0e2701aa1ebaa1f14
   depends:
-  - __osx >=10.13
+  - __osx >=11.0
   - python >=3.12,<3.13.0a0
+  - python >=3.12,<3.13.0a0 *_cpython
   - python_abi 3.12.* *_cp312
   license: BSD-2-Clause
   license_family: BSD
-  size: 60710
-  timestamp: 1756851817591
+  size: 61948
+  timestamp: 1756851912789
 - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
   sha256: 6d9ea2f731e284e9316d95fa61869fe7bbba33df7929f82693c121022810f4ad
   md5: a77f85f77be52ff59391544bfe73390a
@@ -3493,15 +4657,15 @@ packages:
   license_family: MIT
   size: 85189
   timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h4132b18_3.conda
-  sha256: a335161bfa57b64e6794c3c354e7d49449b28b8d8a7c4ed02bf04c3f009953f9
-  md5: a645bb90997d3fc2aea0adf6517059bd
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h925e9cb_3.conda
+  sha256: b03433b13d89f5567e828ea9f1a7d5c5d697bf374c28a4168d71e9464f5dafac
+  md5: 78a0fe9e9c50d2c381e8ee47e3ea437d
   depends:
-  - __osx >=10.13
+  - __osx >=11.0
   license: MIT
   license_family: MIT
-  size: 79419
-  timestamp: 1753484072608
+  size: 83386
+  timestamp: 1753484079473
 - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h3f2d84a_0.conda
   sha256: 4b0b713a4308864a59d5f0b66ac61b7960151c8022511cdc914c0c0458375eca
   md5: 92b90f5f7a322e74468bb4909c7354b5
@@ -3514,16 +4678,16 @@ packages:
   license_family: MIT
   size: 223526
   timestamp: 1745307989800
-- conda: https://conda.anaconda.org/conda-forge/osx-64/yaml-cpp-0.8.0-h92383a6_0.conda
-  sha256: 67d25c3aa2b4ee54abc53060188542d6086b377878ebf3e2b262ae7379e05a6d
-  md5: e15e9855092a8bdaaaed6ad5c173fffa
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-cpp-0.8.0-h784d473_1.conda
+  sha256: 450d4c6ad26bc2c18eb9420261568b86918b118c96ab4a7f2176c352b94101a2
+  md5: 04b9b2b8cc9e14758965758d9c423b34
   depends:
-  - libcxx >=18
-  - __osx >=10.13
+  - libcxx >=19
+  - __osx >=11.0
   license: MIT
   license_family: MIT
-  size: 145204
-  timestamp: 1745308032698
+  size: 136591
+  timestamp: 1785924101870
 - conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.8.1-pyha770c72_0.conda
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   md5: 55a52c71e7919a4951cfc6cccf4fa16f
@@ -3536,6 +4700,28 @@ packages:
   license_family: MIT
   size: 15805
   timestamp: 1749657286268
+- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda
+  sha256: 1ad021f32290e72b70a84dfe0c9b278c61aaa1254f1e1c287d68c32ee4f1093f
+  md5: 89d5edf5d52d3bc1ed4d7d3feef508ba
+  depends:
+  - argparse-dataclass >=2.0.0,<3
+  - dpath >=2.1,<3.0
+  - python >=3.10
+  - pyyaml >=6.0,<7.0
+  license: MIT
+  license_family: MIT
+  size: 16215
+  timestamp: 1764250734338
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+  sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+  md5: ba3dcdc8584155c97c648ae9c044b7a3
+  depends:
+  - python >=3.10
+  - python
+  license: MIT
+  license_family: MIT
+  size: 24190
+  timestamp: 1779159948016
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_1.conda
   sha256: c2bcb8aa930d6ea3c9c7a64fc4fab58ad7bcac483a9a45de294f67d2f447f413
   md5: 02738ff9855946075cbd1b5274399a41
@@ -3550,19 +4736,21 @@ packages:
   license: BSD-3-Clause
   size: 467133
   timestamp: 1762512686069
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.25.0-py312h01f6755_1.conda
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-  md5: d9209ec6445f95fba0c3c64fa4a46216
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.25.0-py312h37e1c23_1.conda
+  sha256: af843b0fe62d128a70f91dc954b2cb692f349a237b461788bd25dd928d0d1ef8
+  md5: 9300889791d4decceea3728ad3b423ec
   depends:
   - python
   - cffi >=1.11
   - zstd >=1.5.7,<1.5.8.0a0
-  - __osx >=10.13
+  - python 3.12.* *_cpython
+  - __osx >=11.0
   - python_abi 3.12.* *_cp312
   - zstd >=1.5.7,<1.6.0a0
   license: BSD-3-Clause
-  size: 462661
-  timestamp: 1762512711429
+  license_family: BSD
+  size: 390920
+  timestamp: 1762512713481
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
   sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
   md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
@@ -3575,13 +4763,13 @@ packages:
   license_family: BSD
   size: 567578
   timestamp: 1742433379869
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.7-h8210216_2.conda
-  sha256: c171c43d0c47eed45085112cb00c8c7d4f0caa5a32d47f2daca727e45fb98dca
-  md5: cd60a4a5a8d6a476b30d8aa4bb49251a
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hf451053_7.conda
+  sha256: da867f5092eb0cb746d353694f0098031fd9817a4ce7d5743121209ae0f406ca
+  md5: 4ec2684c73812cc2c3d78379384a39cc
   depends:
-  - __osx >=10.13
-  - libzlib >=1.3.1,<2.0a0
+  - __osx >=11.0
+  - libzlib >=1.3.2,<2.0a0
   license: BSD-3-Clause
   license_family: BSD
-  size: 485754
-  timestamp: 1742433356230
+  size: 433687
+  timestamp: 1786599629846
diff --git a/pixi.toml b/pixi.toml
index dc98c8410..ff7499ff9 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -3,7 +3,7 @@ authors = ["Mitchell Robert Vollger <mrvollger@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 description = "A Snakemake pipeline for calling FIRE peaks using fibertools-rs."
 name = "FIRE"
-platforms = ["osx-64", "linux-64"]
+platforms = ["osx-arm64", "linux-64"]
 version = "0.2.0"
 
 [tasks]
diff --git a/workflow/envs/env.yaml b/workflow/envs/env.yaml
index bc938e0cc..a7eb1228f 100644
--- a/workflow/envs/env.yaml
+++ b/workflow/envs/env.yaml
@@ -4,13 +4,13 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - samtools==1.21
-  - htslib==1.21
+  - samtools==1.24
+  - htslib==1.24
   - bedtools==2.31.1
   - bioconda::fibertools-rs>=0.13,<0.14
   - hck>=0.9.2
   - bioawk
   - ripgrep
   - csvtk
-  - mosdepth==0.3.7
-  - bioconda::bigtools==0.5.5
+  - mosdepth==0.3.14
+  - bioconda::bigtools==0.5.8
diff --git a/workflow/envs/python.yaml b/workflow/envs/python.yaml
index b72cd8234..1fc89f8cf 100644
--- a/workflow/envs/python.yaml
+++ b/workflow/envs/python.yaml
@@ -8,7 +8,7 @@ dependencies:
   - defopt
   - numpy==1.24 # use this version to avoid cxx errors
   - pandas==1.4 # pandas versions later than this have cxx errors
-  - htslib==1.19.1
+  - htslib==1.20
   - pip
   - pip:
       - polars-lts-cpu[pyarrow]==1.7.1

From c01a153aa7ab7c8787d1fecdee8677537892e1ce Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mvollger@gmail.com>
Date: Thu, 13 Aug 2026 17:53:32 -0700
Subject: [PATCH 17/17] docs: let release-please own the v0.2.0 changelog entry

The generated entry comes from the conventional squash-commit messages
(see the merge instructions in PR #62), avoiding a duplicate section
when the first release PR opens.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 CHANGELOG.md | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6565a6854..5769cd383 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,21 +2,6 @@
 
 All notable changes to this project will be documented in this file.
 
-## v0.2.0
-
-- `min_frac_accessible` now defaults to 0.10: FIRE peaks must have at least 10%
-  of reads accessible in addition to passing FDR peak calling (set to 0.0 to
-  restore the old behavior)
-- Update fibertools-rs to 0.13.x (requires `ft pileup --rgn`; also updates samtools,
-  htslib, and bedtools pins in `workflow/envs/env.yaml`)
-- Polars fixes: explicit schemas for chrom/score columns (#48, #52, #53, #56)
-- `exclude_from_shuffle` now works when no `excludes` are configured (non-hg38 refs)
-- Test data now downloaded via rclone; test runs start from a clean state
-  (`test-clean` task added)
-- Mac support moved from Intel (osx-64) to Apple Silicon (osx-arm64), following
-  bioconda's fibertools-rs builds; samtools/htslib 1.24, mosdepth 0.3.14,
-  bigtools 0.5.8
-
 ## v0.1.2
 
 - fix #34