40 lines
1.2 KiB
Plaintext
40 lines
1.2 KiB
Plaintext
import os
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from dotenv import load_dotenv
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load_dotenv()
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configfile: "config/main.yaml"
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configfile: "config/dependencies.yaml"
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configfile: "../reference/species_list.yaml"
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module preparation:
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snakefile: "rules/preparation.smk"
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config: config
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module baseline:
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snakefile: "rules/baseline_pipeline.smk"
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config: config
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module ml:
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snakefile: 'rules/ml_pipeline.smk'
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config: config
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# Pulldown
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rule all:
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input:
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#"binaries/datasets",
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#f"{config['dorado_model_dir']}/{config['fast_model_name']}",
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#f"{config['dorado_model_dir']}/{config['hac_model_name']}",
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#'../data/reference_genomes/full_reference.mmi',
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#'../data/raw_pod5/'
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#'../data/pod5_files_to_pull',
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#'../data/basecalled_reads/hac.fastq.gz'
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#expand('../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
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'../data/aligned_reads/nomiss_hac_to_genome.sorted.bam',
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'../data/aligned_reads/trap_hac_to_genome.sorted.bam'
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#'../data/ml_inputs/hac_label_store.pq'
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#'../data/ml_inputs/model_layouts/cnn_512_4_100000_11_4.json'
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use rule * from preparation
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use rule * from baseline
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use rule * from ml
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