biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/scripts/bam/CNVpytor.py

@@ -1,26 +1,26 @@
 from pathlib import Path
 
+import warnings
 import pandas
-from biopipen.scripts.vcf.VcfFix_utils import HeaderContig, fix_vcffile
+from datetime import datetime
+from diot import Diot  # pyright: ignore
 from biopipen.utils.reference import bam_index
-from biopipen.utils.misc import run_command, dict_to_cli_args
+from biopipen.utils.misc import run_command, dict_to_cli_args, logger
 
-bamfile = {{in.bamfile | quote}}  # pyright: ignore
-snpfile = {{in.snpfile | repr}}  # pyright: ignore
+bamfile: str = {{in.bamfile | quote}}  # pyright: ignore # noqa
+snpfile: str = {{in.snpfile | quote}}  # pyright: ignore
 outdir = Path({{out.outdir | quote}})  # pyright: ignore
-cnvpytor = {{envs.cnvpytor | quote}}  # pyright: ignore
-cnvnator2vcf = {{envs.cnvnator2vcf | quote}}  # pyright: ignore
-samtools = {{envs.samtools | quote}}  # pyright: ignore
-ncores = {{envs.ncores | int}}  # pyright: ignore
+cnvpytor: str = {{envs.cnvpytor | quote}}  # pyright: ignore
+samtools: str = {{envs.samtools | quote}}  # pyright: ignore
+ncores: int = {{envs.ncores | int}}  # pyright: ignore
 refdir = {{envs.refdir | quote}}  # pyright: ignore
 genome = {{envs.genome | quote}}  # pyright: ignore
-chrsize = {{envs.chrsize | quote}}  # pyright: ignore
-filters = {{envs.filters | repr}}  # pyright: ignore
-args = {{envs | repr}}  # pyright: ignore
+chrsize: str = {{envs.chrsize | quote}}  # pyright: ignore
+filters: dict = {{envs.filters | repr}}  # pyright: ignore
+args: Diot = {{envs | repr}}  # pyright: ignore
 
 del args['cnvpytor']
 del args['ncores']
-del args['cnvnator2vcf']
 del args['samtools']
 del args['refdir']
 del args['genome']
@@ -28,7 +28,7 @@ del args['chrsize']
 del args['filters']
 
 
-bamfile = bam_index(bamfile, outdir, samtools, ncores)
+bamfile: Path = bam_index(bamfile, str(outdir), samtools, ncores=ncores)
 
 NOSNP_COLS = [
     "CNVtype",
@@ -236,47 +236,138 @@ def load_chrsize():
                 yield chrom, int(size)
 
 
-def cnvpytor2vcf(infile, snp, fix=True):
-    unfixedfile = Path(infile).with_suffix(f".unfixed.vcf")
-    outfile = Path(infile).with_suffix(f".vcf")
-    stdout = run_command(
-        dict_to_cli_args(
-            {
-                "": cnvpytor2vcf,
-                "reference": genome,
-                "_": [infile, refdir],
-            },
-            prefix="-",
-        ),
-        stdout="return",
-    )
-    if fix:
-        unfixedfile.write_text(stdout)
+def parse_chrom(chrom, chromdir):
+    file = Path(chromdir) / f"{chrom}.fa"
+    if not file.exists():
+        warnings.warn(f"Chromosome file not found in refdir: {chrom}")
+        return ""
 
-        fixes = [
-            {
-                "kind": "format",
-                "id": "PE",
-                "fix": lambda obj: setattr(obj, 'Type', 'String')
-            },
-            {
-                "kind": "fields",
-                "fix": lambda items: items.__setitem__(-1, Path(bamfile).stem)
-            }
-        ]
+    seq = ""
+    with open(file) as f:
+        for line in f:
+            line = line.strip()
+            if not line:
+                continue
+            if line.startswith(">"):
+                seq = ""
+            else:
+                seq += line
+    return seq
+
+
+def cnvpytor2vcf(infile, snp):
+    # snp: in case to be used in the future
+    outfile = Path(infile).with_suffix(f".vcf")
+    # stdout = run_command(
+    #     dict_to_cli_args(
+    #         {
+    #             "": cnvnator2vcf,
+    #             "reference": genome,
+    #             "_": [infile, refdir],
+    #         },
+    #         prefix="-",
+    #     ),
+    #     stdout="return",
+    # )
+    ## command hangs
+    with open(infile) as fin, open(outfile, "w") as fout:
+        fout.write("##fileformat=VCFv4.2\n")
+        fout.write(f"##fileDate={datetime.now().strftime('%Y%m%d')}\n")
+        fout.write(f"##reference={genome}\n")
+        fout.write(f"##source=CNVpytor\n")
         for chrom, size in load_chrsize():
-            fixes.append({
-                "kind": "contig",
-                "append": True,
-                "fix": (
-                    lambda obj, chrom=chrom, size=size:
-                    HeaderContig(ID=chrom, length=size)
-                )
-            })
+            fout.write(f"##contig=<ID={chrom},length={size}>\n")
+        fout.write('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n')
+        fout.write('##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n')
+        fout.write('##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">\n')
+        fout.write('##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n')
+        fout.write('##INFO=<ID=natorRD,Number=1,Type=Float,Description="Normalized RD">\n')
+        fout.write('##INFO=<ID=natorP1,Number=1,Type=Float,Description="e-val by t-test">\n')
+        fout.write('##INFO=<ID=natorP2,Number=1,Type=Float,Description="e-val by Gaussian tail">\n')
+        fout.write('##INFO=<ID=natorP3,Number=1,Type=Float,Description="e-val by t-test (middle)">\n')
+        fout.write('##INFO=<ID=natorP4,Number=1,Type=Float,Description="e-val by Gaussian tail (middle)">\n')
+        fout.write('##INFO=<ID=natorQ0,Number=1,Type=Float,Description="Fraction of reads with 0 mapping quality">\n')
+        fout.write('##INFO=<ID=natorPE,Number=1,Type=Integer,Description="Number of paired-ends support the event">\n')
+        fout.write('##INFO=<ID=SAMPLES,Number=.,Type=String,Description="Sample genotyped to have the variant">\n')
+        fout.write('##ALT=<ID=DEL,Description="Deletion">\n')
+        fout.write('##ALT=<ID=DUP,Description="Duplication">\n')
+        fout.write('##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n')
+        fout.write('##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">\n')
+        fout.write('##FORMAT=<ID=PE,Number=1,Type=String,Description="Number of paired-ends that support the event">\n')
+        fout.write(f"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t{bamfile.stem}\n")
+        prev_chrom, chrom_seq, count = "", "", 0
+        for line in fin:
+            # type, coor, length, rd, p1, p2, p3, p4, q0, pe = line.strip("\n").split()
+            items = line.strip("\n").split()
+            type, coor, length = items[:3]
+            rd = float(items[3]) if len(items) > 3 else False
+            p1 = items[4] if len(items) > 4 else ""
+            p2 = items[5] if len(items) > 5 else ""
+            p3 = items[6] if len(items) > 6 else ""
+            p4 = items[7] if len(items) > 7 else ""
+            q0 = items[8] if len(items) > 8 else ""
+            pe = items[9] if len(items) > 9 else ""
+            chrom, pos = coor.split(":")
+            start, end = pos.split("-")
+            start, end = int(start), int(end)
+            is_del = type == "deletion"
+            is_dup = type == "duplication"
+
+            if not is_del and not is_dup:
+                warnings.warn(f"Skipping unrecognized CNV type: {type}")
+                continue
 
-        fix_vcffile(unfixedfile, outfile, fixes)
-    else:
-        outfile.write_text(stdout)
+            if chrom != prev_chrom:
+                chrom_seq = parse_chrom(chrom, refdir)
+                prev_chrom = chrom
+
+            count += 1
+            info = f"END={end}"
+            info += f";SVTYPE=DEL;SVLEN=-{length}" if is_del else f";SVTYPE=DUP;SVLEN={length}"
+            info += ";IMPRECISE"
+            info += f";natorRD={rd}" if rd is not False else ""
+            info += f";natorP1={p1}" if p1 else ""
+            info += f";natorP2={p2}" if p2 else ""
+            info += f";natorP3={p3}" if p3 else ""
+            info += f";natorP4={p4}" if p4 else ""
+            info += f";natorQ0={q0}" if q0 else ""
+            info += f";natorPE={pe}" if pe else ""
+
+            gt = "GT"
+            if rd is not False:
+                gt += ":CN"
+                gt += ":PE" if pe else ""
+                gt += "\t"
+                if is_del and rd < 0.25:
+                    gt += "1/1:0"
+                elif is_del and rd >= 0.25:
+                    gt += "0/1:1"
+                elif rd <= 1.75:
+                    gt += "0/1:2"
+                elif rd > 1.75 and rd <= 2.25:
+                    gt += "1/1:2"
+                elif rd > 2.25:
+                    gt += f"./2:{rd:.0f}"
+                else:
+                    gt = "GT:PE\t./." if pe else "GT\t./."
+
+                gt += f":{pe}" if pe else ""
+            else:
+                gt += "\t./."
+
+            fout.write("\t".join(
+                [
+                    chrom,
+                    str(start),
+                    f"CNVpytor_{'del_' if is_del else 'dup_'}{count}",
+                    chrom_seq[start - 1] if start < len(chrom_seq) else "N",
+                    "<DEL>" if is_del else "<DUP>",
+                    ".",
+                    "PASS",
+                    info,
+                    gt,
+                ]
+            ) + "\n")
 
 
 def do_case():
@@ -290,7 +381,7 @@ def do_case():
     rootfile = outdir / "file.pytor"
     case["j"] = case.get("j", ncores)
 
-    # read depth signal
+    logger.info("Reading depth signals ...")
     run_command(
         dict_to_cli_args(
             {
@@ -305,7 +396,7 @@ def do_case():
         fg=True,
     )
 
-    # predicting cnv
+    logger.info("Predicting CNVs ...")
     run_command(
         dict_to_cli_args(
             {
@@ -314,6 +405,7 @@ def do_case():
                 "his": binsizes,
             },
             prefix="-",
+            dup_key=False,
         ),
         fg=True,
     )
@@ -326,6 +418,7 @@ def do_case():
                 "partition": binsizes,
             },
             prefix="-",
+            dup_key=False,
         ),
         fg=True,
     )
@@ -336,6 +429,7 @@ def do_case():
         mask_snps = snp.pop("mask_snps", True)
         baf_nomask = snp.pop("baf_nomask", False)
 
+        logger.info("Importing SNP data ...")
         run_command(
             dict_to_cli_args(
                 {
@@ -350,6 +444,7 @@ def do_case():
         )
 
         if mask_snps:
+            logger.info("Masking 1000 Genome SNPs ...")
             run_command(
                 dict_to_cli_args(
                     {
@@ -362,6 +457,7 @@ def do_case():
                 fg=True,
             )
 
+        logger.info("Calculating BAF histograms ...")
         run_command(
             dict_to_cli_args(
                 {
@@ -375,8 +471,9 @@ def do_case():
             fg=True,
         )
 
-    # call
+    logger.info("Predicting CNV regions using joint caller ...")
     for binsize in binsizes:
+        logger.info(f"- binsize: {binsize}")
         outfile = outdir / f"calls{'.combined' if snp is not False else ''}.{binsize}.tsv"
         outfile_filtered = outdir / f"calls{'.combined' if snp is not False else ''}.{binsize}.filtered.tsv"
         run_command(
@@ -392,6 +489,7 @@ def do_case():
             stdout=outfile,
         )
 
+        logger.info("  Converting to other formats ...")
         cnvpytor2other(outfile, bool(snp), "gff")
         cnvpytor2other(outfile, bool(snp), "bed")
         cnvpytor2vcf(outfile, bool(snp))
@@ -424,6 +522,7 @@ def do_case():
         cnvpytor2vcf(outfile_filtered, bool(snp))
 
         # plots
+        logger.info("  Plotting ...")
         manplot = outdir / f"manhattan.{binsize}.png"
         run_command(
             dict_to_cli_args(

biopipen/scripts/bam/ControlFREEC.py

@@ -1,24 +1,23 @@
 import os
 import glob
-import rtoml
 import shutil
-from diot import Diot
+from diot import Diot  # type: ignore
 from biopipen.utils.misc import dict_to_cli_args, run_command
 
-bamfile = {{ in.bamfile | repr }}  # pyright: ignore
-snpfile = {{ in.snpfile | repr }}  # pyright: ignore
-outdir = {{ out.outdir | repr }}  # pyright: ignore
-freec = {{ envs.freec | repr }}  # pyright: ignore
+bamfile = {{ in.bamfile | quote }}  # pyright: ignore # noqa
+snpfile = {{ in.snpfile | quote }}  # pyright: ignore
+outdir = {{ out.outdir | quote }}  # pyright: ignore
+freec: str = {{ envs.freec | repr }}  # pyright: ignore
 ncores = {{ envs.ncores | repr }}  # pyright: ignore
 bedtools = {{ envs.bedtools | repr }}  # pyright: ignore
 sambamba = {{ envs.sambamba | repr }}  # pyright: ignore
 samtools = {{ envs.samtools | repr }}  # pyright: ignore
 tabix = {{ envs.tabix | repr }}  # pyright: ignore
-rscript = {{ envs.rscript | repr }}  # pyright: ignore
-ref = {{ envs.ref | repr }}  # pyright: ignore
-refdir = {{ envs.refdir | repr }}  # pyright: ignore
+rscript: str = {{ envs.rscript | repr }}  # pyright: ignore
+ref = {{ envs.ref | quote }}  # pyright: ignore
+refdir = {{ envs.refdir | quote }}  # pyright: ignore
 binsize = {{ envs.binsize | repr }}  # pyright: ignore
-args = {{ envs.args | repr }}  # pyright: ignore
+args = {{ envs.args | dict }}  # pyright: ignore
 
 chrLenFile = f"{ref}.fai"
 if snpfile:
@@ -33,7 +32,7 @@ if snpfile:
             }
         ),
         stdout="return",
-    ).strip().splitlines()
+    ).strip().splitlines()  # type: ignore
 
     kept_seqs = []
     with open(chrLenFile, "r") as fin, open(chrLenFile2, "w") as fout:
@@ -79,7 +78,7 @@ config.BAF |= Diot(
 
 os.makedirs(f"{outdir}/FREEC-output", exist_ok=True)
 
-config_ini = rtoml.dumps(config).replace('"', "")
+config_ini = config.to_toml().replace('"', "")   # type: ignore
 
 with open(configfile, "w") as fconf:
     fconf.write(config_ini)
@@ -92,7 +91,7 @@ run_command(
 
 # plot cnvs
 # get makeGraph.R
-freec_path = os.path.realpath(shutil.which(freec).strip())
+freec_path = os.path.realpath(shutil.which(freec).strip())  # type: ignore
 mkgraph = os.path.join(os.path.dirname(freec_path), "makeGraph.R")
 if not os.path.exists(mkgraph):
     raise RuntimeError("makeGraph.R not found")
@@ -102,7 +101,7 @@ try:
 except IndexError:
     raise RuntimeError("Control-FREEC failed to run") from None
 
-rscript_path = os.path.realpath(shutil.which(rscript).strip())
+rscript_path = os.path.realpath(shutil.which(rscript).strip())  # type: ignore
 rpath = os.path.join(os.path.dirname(rscript_path), "R")
 
 plotcmd = f"cat {mkgraph} | R --slave --args {config.general.ploidy} {ratiofile}"

biopipen/scripts/bam/SamtoolsView.py

@@ -0,0 +1,33 @@
+from pathlib import PosixPath  # type: ignore # noqa
+from biopipen.utils.misc import run_command, dict_to_cli_args
+from biopipen.utils.reference import bam_index
+
+bamfile: str = {{ in.bamfile | quote }}  # pyright: ignore # noqa
+outfile: str = {{ out.outfile | quote }}  # pyright: ignore # noqa
+envs: dict = {{envs | attr: "to_dict" | call}}  # pyright: ignore  # noqa
+ncores = envs.pop("ncores")
+samtools = envs.pop("samtools")
+should_index = envs.pop("index")
+
+
+def run_samtools(infile):
+    cmd = [
+        samtools,
+        "view",
+        "-b",
+        "--threads",
+        str(ncores),
+        "-o",
+        outfile,
+    ] + dict_to_cli_args(envs, dashify=True) + [infile]
+
+    run_command(cmd, fg=True)
+    if should_index:
+        bam_index(outfile, tool="samtools", samtools=samtools, ncores=ncores)
+
+    return outfile
+
+
+if __name__ == "__main__":
+    infile = bam_index(bamfile, tool="samtools", samtools=samtools, ncores=ncores)
+    run_samtools(infile)

biopipen/scripts/bed/Bed2Vcf.py

@@ -8,14 +8,14 @@ from pysam import FastaFile
 
 from biopipen.utils.misc import run_command
 
-inbed = {{in.inbed | quote}}  # pyright: ignore
-outvcf = {{out.outvcf | quote}}  # pyright: ignore
-tmpoutvcf = {{out.outvcf | append: ".tmp" | quote}}  # pyright: ignore
+inbed: str = {{in.inbed | quote}}  # pyright: ignore # noqa
+outvcf: str = {{out.outvcf | quote}}  # pyright: ignore
+tmpoutvcf: str = {{out.outvcf | str | append: ".tmp" | quote}}  # pyright: ignore
 joboutdir = Path({{job.outdir | quote}})  # pyright: ignore
-ref = {{envs.ref | quote}}  # pyright: ignore
+ref: str = {{envs.ref | quote}}  # pyright: ignore
 headers = {{envs.headers | repr}}  # pyright: ignore
 infos = {{envs.infos | repr}}  # pyright: ignore
-base = {{envs.base | int}}  # pyright: ignore
+base: int = {{envs.base | int}}  # pyright: ignore
 formats = {{envs.formats | repr}}  # pyright: ignore
 index = {{envs.index | repr}}  # pyright: ignore
 bcftools = {{envs.bcftools | quote}}  # pyright: ignore

biopipen/scripts/bed/BedConsensus.py

@@ -1,16 +1,16 @@
 import sys
 from math import ceil
-from pathlib import Path
+from pathlib import Path, PosixPath  # noqa: F401
 
 from biopipen.utils.misc import run_command
 
-bedfiles = {{in.bedfiles | repr}}  # pyright: ignore
-outfile = Path({{out.outbed | repr}})  # pyright: ignore
+bedfiles: list[Path] = {{in.bedfiles | each: as_path}}  # pyright: ignore # noqa
+outfile = Path({{out.outbed | quote}})  # pyright: ignore
 bedtools_path = {{envs.bedtools | repr}}  # pyright: ignore
-cutoff = {{envs.cutoff | repr}}  # pyright: ignore
+cutoff: float = {{envs.cutoff | repr}}  # pyright: ignore
 distance = {{envs.distance | repr}}  # pyright: ignore
 chrsize = {{envs.chrsize | repr}}  # pyright: ignore
-bedfiles = [Path(bedfile) for bedfile in bedfiles]
+# bedfiles = [Path(bedfile) for bedfile in bedfiles]
 # In case there are duplicated stems
 stems = [f"{bedfile.stem}__{i}" for i, bedfile in enumerate(bedfiles)]
 

biopipen/scripts/bed/BedLiftOver.sh

@@ -1,11 +1,13 @@
+# shellcheck disable=SC2148,SC1083
 inbed={{ in.inbed | quote }}
 outbed={{ out.outbed | quote }}
 rejfile={{ job.outdir | joinpaths: "rejected.bed" | quote }}
 liftover={{ envs.liftover | quote }}
 chain={{ envs.chain | quote }}
 
+# shellcheck disable=SC2154
 $liftover \
-    $inbed \
-    $chain \
-    $outbed \
-    $rejfile
+    "$inbed" \
+    "$chain" \
+    "$outbed" \
+    "$rejfile"

biopipen/scripts/bed/BedtoolsIntersect.py

@@ -0,0 +1,54 @@
+from pathlib import Path
+from biopipen.utils.misc import run_command, dict_to_cli_args, logger
+
+afile = Path({{in.afile | quote}})  # pyright: ignore # noqa: #999
+bfile = Path({{in.bfile | quote}})  # pyright: ignore
+outfile: str = {{out.outfile | quote}}  # pyright: ignore
+envs: dict = {{envs | dict}}  # pyright: ignore
+
+bedtools = envs.pop("bedtools")
+sort = envs.pop("sort")
+chrsize = envs.pop("chrsize")
+postcmd = envs.pop("postcmd", None)
+outdir = Path(outfile).parent
+
+if chrsize and "g" in envs:
+    logger.warning("Ignoring envs.g because envs.chrsize is provided.")
+    envs["g"] = Path(chrsize).expanduser()
+elif chrsize:
+    envs["g"] = Path(chrsize).expanduser()
+
+if sort:
+    afile_sorted = outdir / f"{afile.stem}_sorted{afile.suffix}"
+    bfile_sorted = outdir / f"{bfile.stem}_sorted{bfile.suffix}"
+    run_command(
+        [bedtools, "sort", "-g", envs["g"], "-i", afile],
+        stdout=afile_sorted,
+    )
+    run_command(
+        [bedtools, "sort", "-g", envs["g"], "-i", bfile],
+        stdout=bfile_sorted,
+    )
+    afile = afile_sorted
+    bfile = bfile_sorted
+
+envs[""] = [bedtools, "intersect"]
+envs["a"] = afile
+envs["b"] = bfile
+envs.setdefault("sorted", True)
+
+if envs["sorted"] and not "g" in envs:
+    raise ValueError("envs.g is required or manullay set envs.sorted to False.")
+
+if postcmd:
+    ofile = Path(outfile).with_suffix(".prior.bt")
+    run_command(dict_to_cli_args(envs, prefix="-"), stdout=ofile)
+    postcmd_file = outdir / "_postcmd.sh"
+    postcmd_file.write_text(postcmd)
+    run_command(
+        ["bash", postcmd_file],
+        env={"infile": ofile, "outfile": outfile, "outdir": outdir},
+        fg=True,
+    )
+else:
+    run_command(dict_to_cli_args(envs, prefix="-"), stdout=outfile)

biopipen/scripts/bed/BedtoolsMakeWindows.py

@@ -0,0 +1,47 @@
+from pathlib import Path
+from biopipen.utils.misc import run_command, logger
+
+infile = Path({{in.afile | quote}})  # pyright: ignore # noqa: #999
+outfile = Path({{in.bfile | quote}})  # pyright: ignore
+bedtools: str = {{envs.bedtools | quote}}  # pyright: ignore
+window = {{envs.window | repr}}  # pyright: ignore
+step = {{envs.step | repr}}  # pyright: ignore
+nwin = {{envs.nwin | repr}}  # pyright: ignore
+reverse = {{envs.reverse | repr}}  # pyright: ignore
+name = {{envs.name | repr}}  # pyright: ignore
+
+if nwin is None and window is None:
+    raise ValueError("Either `nwin` or `window` should be provided.")
+
+if nwin is not None and window is not None:
+    raise ValueError("Either `nwin` or `window` should be provided, not both.")
+
+# detect if infile is a genome size file or a bed file
+with infile.open() as f:
+    line = f.readline().strip()
+    if len(line.split("\t")) > 2:
+        is_bed = True
+    else:
+        is_bed = False
+
+if is_bed:
+    logger.info("BED file is detected as input.")
+    cmd = [bedtools, "makewindows", "-b", infile]
+else:
+    logger.info("Genome size file is detected as input.")
+    cmd = [bedtools, "makewindows", "-g", infile]
+
+if nwin:
+    cmd.extend(["-n", nwin])
+elif step is not None:
+    cmd.extend(["-w", window, "-s", step])
+else:
+    cmd.extend(["-w", window])
+
+if reverse:
+    cmd.append("-reverse")
+
+if name != "none":
+    cmd.extend(["-name", name])
+
+run_command(cmd, stdout=outfile)

biopipen/scripts/bed/BedtoolsMerge.py

@@ -1,8 +1,8 @@
-from biopipen.utils import run_command, dict_to_cli_args
+from biopipen.utils.misc import run_command, dict_to_cli_args
 
-inbed = {{in.inbed | repr}}  # pyright: ignore
-outbed = {{out.outbed | repr}}  # pyright: ignore
-envs = {{envs | repr}}  # pyright: ignore
+inbed = {{in.inbed | quote}}  # pyright: ignore # noqa: #999
+outbed = {{out.outbed | quote}}  # pyright: ignore
+envs: dict = {{envs | dict}}  # pyright: ignore
 bedtools = envs.pop("bedtools", "bedtools")
 
 envs[""] = [bedtools, "merge"]