Fix pipeline DAG

[lina-kim]

Closes #58. Fixes the empty channel from unused process issue. Some fixes still needed to resolve Cutadapt's overlapping samples issue.

Runs to completion locally with a combination of Conda and Docker, but this should be streamlined ideally by #7. Runs fine on HPC with Docker alone.

Config file used:

params {
    read_type = "paired"
    fondue_conda_env = "/anaconda3/envs/fondue"
    inp_id_file = "data/sra_ids.tsv"
    email_address = "lina.kim@hest.ethz.ch"
    primer_file = "data/all_primers.tsv"

    classifier {
        num_jobs = 1
    }
}

process {
    withName:CLASSIFY_TAXONOMY {
        cpus = 6
        memory = 16.GB
        conda = "/anaconda3/envs/qiime2-2023.2"
    }
}
conda.enabled = true
docker.enabled = true
singularity.enabled = false