cleanup: rm workflow/rules/basecalling.smk because it is part of workflow_fast5

workflow/rules/basecalling.smk

-# Basecalling
-checkpoint guppy_gpu_basecalling:
-    input:
-        # expand(os.path.join(RESULTS_DIR, "input/metag/ont/{fast5}"), fast5=[os.path.basename(f) for f in INPUT_G_LR_FAST5])
-        os.path.join(RESULTS_DIR, "input/metag/ont")
-    output:
-        directory(os.path.join(RESULTS_DIR, "preproc/metag/lr/checkpoints"))
-    log:
-        out="logs/guppy.metag.lr.out.log",
-        err="logs/guppy.metag.lr.err.log"
-    threads:
-        config["guppy"]["gpu"]["threads"]
-    message:
-        "Preprocessing long reads: Basecalling w/ Guppy"
-    shell:
-        """
-        (date && \
-        {config[guppy][gpu][bin]} --input_path {input} --save_path {output} \
-        --config {config[guppy][config]} \
-        --disable_pings --compress_fastq \
-        --cpu_threads_per_caller {threads} \
-        -x {config[guppy][gpu][gpu_device]} \
-        --records_per_fastq {config[guppy][gpu][records_per_fastq]} \
-        --chunk_size {config[guppy][gpu][chunk_size]} \
-        --chunks_per_runner {config[guppy][gpu][chunks_per_runner]} \
-        --gpu_runners_per_device {config[guppy][gpu][runners_per_device]} \
-        --num_callers {config[guppy][gpu][num_callers]} && \
-        date) 2>> {log.err} >> {log.out}
-        """
-
-def aggregate_guppy_basecalling(wildcards):
-    checkpoint_output = checkpoints.guppy_gpu_basecalling.get(**wildcards).output[0]
-    return expand(
-        os.path.join(RESULTS_DIR, "preproc/metag/lr/checkpoints/fastq_runid_{runid_i_j}.fastq.gz"),
-        runid_i_j=glob_wildcards(os.path.join(checkpoint_output, "fastq_runid_{runid_i_j}.fastq.gz")).runid_i_j,
-    )
-
-rule merge_guppy_basecalling:
-    input:
-        aggregate_guppy_basecalling
-    output:
-        os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.fastq.gz")
-    message:
-        "Preprocessing long reads: Cat FASTQ"
-    shell:
-        "cat $(echo \"{input}\" | sort) > {output}"