feat: update fibertools version

.github/workflows/main.yml

@@ -12,8 +12,8 @@ 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: v0.37.0
+          pixi-version: v0.66.0
           cache: true
       - run: pixi run test

CHANGELOG.md

@@ -1,6 +1,10 @@
 # Change Log
 
 All notable changes to this project will be documented in this file.
+## v0.2.0
+- Update fibertools-rs version (also samtools, htslib, and bedtools) in `workflow/envs/env.yaml`
+- Fix Polars issue in #52
+
 
 ## v0.1.2
 

pixi.toml

@@ -1,41 +1,16 @@
-[project]
+[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",
-    "$INIT_CWD",
-    "&&",
-    "mkdir",
-    "-p",
-    "fire-test-data",
-    "&&",
-    "aws",
-    "s3",
-    "--no-sign-request",
-    "sync",
-    "--endpoint-url",
-    "https://s3.kopah.orci.washington.edu",
-    "s3://stergachis/public/FIRE/test-data",
-    "fire-test-data/",
-] }
-test = { cmd = [
-    "cd",
-    "$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 "$INIT_CWD/fire-test-data" && aws s3 --no-sign-request sync --endpoint-url https://s3.kopah.orci.washington.edu s3://stergachis/public/FIRE/test-data "$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" && trap "rm -rf results temp .snakemake" EXIT && snakemake -s "$PIXI_PROJECT_ROOT/workflow/Snakefile" --configfile test.yaml -k' ''', depends-on = [
     "test-data",
 ], clean-env = true }
 fire = { cmd = [

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>=1.19.1
+  - htslib>=1.19.1
+  - bedtools>=2.31
+  - bioconda::fibertools-rs==0.9
   - hck>=0.9.2
   - bioawk
   - ripgrep

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
+                zcat -f {params.exclude}
+            fi
         ) \
             | cut -f 1-3 \
             | bedtools sort \

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} -r {wildcards.chrom} -t {threads} \
             --fiber-coverage --shuffle {input.shuffled} \
             --no-msp --no-nuc \
             | bgzip -@ {threads} \
@@ -103,7 +103,7 @@ rule pileup_chromosome:
         """
         {FT_EXE} pileup -t {threads} \
             --haps --fiber-coverage \
-            {input.bam} {wildcards.chrom} \
+            {input.bam} -r {wildcards.chrom} \
             | bgzip -@ {threads} \
             > {output.bed}
         """

workflow/scripts/fdr-table.py

@@ -57,11 +57,16 @@ def read_pileup_file(infile, nrows):
             return None
 
     # 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. 
     schema_overrides = {}
-    for n in ["score", "score_H1", "score_H2", "score_shuffled"]:
-        if n in header:
-            schema_overrides[n] = float
-
+    for col_idx, col_name in enumerate(header, start=1):
+        positional = f"column_{col_idx}"
+        if col_name in ("score", "score_H1", "score_H2", "score_shuffled"):
+            schema_overrides[positional] = pl.Float64
+        elif col_name == "#chrom":
+            schema_overrides[positional] = pl.Utf8
     logging.info(f"Header of the pileup file:\n{header}")
     logging.info(f"Schema overrides for the pileup file:\n{schema_overrides}")
 

workflow/scripts/merge_fire_peaks.py

@@ -124,7 +124,7 @@ def main(
     logger.setLevel(log_level)
 
     inf = io.StringIO(sys.stdin.read())
-    df = pl.read_csv(inf, separator="\t", null_values=".")
+    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