intial version

workflow/rules/baseline_pipeline.smk

@@ -0,0 +1,68 @@
+def get_model_name(wildcards):
+    config_param=f'{wildcards.model}_model_name'
+    return config[config_param]
+
+def get_model_requirement(wildcards):
+    return f"{config['dorado_model_dir']}/{config[f'{wildcards.model}_model_name']}
+
+def get_benchmarking_file(wildcards):
+    config_param = f'{wildcards.model}_benchmarks_file'
+    if config[config_param]:
+        return f'--batchsize-benchmarks-file {config[config_param]}'
+    return ''
+
+def get_qscore(wildcards):
+    config_param = f'{wildcards.model}_min_q'
+    if config[config_param]:
+        return f'--min-qscore {config[config_param]}'
+    return ''
+
+def get_batch_names(input_file):
+    with open(input_file,'rt') as ih:
+        return [line.strip().split('/')[-1].split('.')[0] for line in ih]
+
+rule download_pod5:
+    output:
+        '../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5'
+    threads: 1
+    wildcard_constraints:
+        batch="\d+"
+    shell:
+        """
+        aws s3 cp --no-sign-request s3://ont-open-data/nomiss_96BC_P2I_SUP_2026/raw/pod5/PBK98658_853a956f_57f83f46_{wildcards.batch}.pod5 {output}
+        """
+
+rule basecall_pod5:
+    input:
+        pod5='../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',
+        model=get_model_requirement
+    output:
+        '../data/basecalled_reads/{model}/PBK98658_853a956f_57f83f46_{batch}.fastq.gz'
+    threads:
+        32
+    resources:
+        gpu=1
+    params:
+        benchmarking=get_benchmarking_file,
+        min_qscore=get_qscore,
+        dorado_model=get_model_name
+    wildcard_constraints:
+        batch="\d+",
+        model="hac|fast"
+    shell:
+        """
+        dorado basecaller --models-directory {config[dorado_model_dir]} --emit-fastq {params.benchmarking} {params.min_qscore} {params.dorado_model} {input.pod5} > {output}
+        """
+
+rule concatenate_basecalled_fastq:
+    input:
+        expand('../data/basecalled_reads/{{model}}/PBK98658_853a956f_57f83f46_{batch}.fastq.gz',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
+    output:
+        '../data/basecalled_reads/{model}.fastq.gz'
+    threads: 1
+    wildcard_constraints:
+        model="hac|fast"
+    shell:
+        """
+        zcat {input} > {output}
+        """