basecall_dorado/Snakefile at main · EichlerLab/basecall_dorado · GitHub

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"""
Basecall ONT runs from FAST5.

Adopted from https://github.com/paudano/ont_basecall
"""

### Libraries ###

import datetime
import numpy as np
import os, sys
import pandas as pd
import shutil
import time
import getpass
import glob

### Get install directory ###


INSTALL_DIR = os.path.dirname(workflow.snakefile)


configfile: os.path.join(INSTALL_DIR, "config/config.json")


### Setup cell table ###

CELL_DF_FILE_NAME = config.get("cell_table", "ont_basecall.tsv")

CELL_DF = pd.read_csv(
    CELL_DF_FILE_NAME, sep="\t", index_col=["SAMPLE", "SEQ_TYPE", "RUN_ID", "PROFILE"]
)

detected_dorado_version = [ dorado_path.split("/")[8] for dorado_path in glob.glob("/net/eichler/vol28/7200/software/modules-sw/dorado/*/Linux/Ubuntu22.04/x86_64/bin/dorado") ]

### Includes ###

shell.prefix("source ~/.bash_profile; ")

wildcard_constraints:
    sample="|".join(CELL_DF.index.get_level_values("SAMPLE")),
    seq_type="|".join(CELL_DF.index.get_level_values("SEQ_TYPE")),
    run_id="|".join(CELL_DF.index.get_level_values("RUN_ID")),
    profile="|".join(list(config["profile"].keys())),
    modbase="|".join(list(config["mod_base_profile"].keys())),
    version_dash = "|".join(detected_dorado_version)

include: "rules/basecall.snake"


localrules:
    basecall_all,


rule basecall_all:
    input:
        _gather_dorado_files,