tc.txt

#!/bin/bash

# Replace ProkEvo_dir with the absolute path to the current directory

tr ex_conda_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/create_conda_env.sh"
    }
}

tr ex_sra_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/download_sra.sh"
    }
}

tr ex_trim_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/trim.sh"
    }
}

tr ex_fastqc_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/fastqc.sh"
    }
}

tr ex_fastqc_fail_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/fastqc_fail.sh"
    }
}

tr ex_spades_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/spades.sh"
    }
}

tr ex_quast_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/quast.sh"
    }
}

tr ex_filtering_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/filtering.sh"
    }
}

tr ex_sistr_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/sistr.sh"
    }
}

tr ex_merge_sistr {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/merge_sistr.sh"
    }
}

tr ex_mlst_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/mlst.sh"
    }
}

tr ex_plasmidfinder_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/plasmidfinder.sh"
    }
}

tr ex_abricate_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/abricate.sh"
    }
}

tr ex_prokka_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/prokka.sh"
    }
}

tr ex_roary_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/roary.sh"
    }
}

tr ex_fastbaps_run {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/fastbaps.sh"
    }
}

tr ex_cat {
    site local-hcc {
        pfn "/bin/cat"
    }
}

tr ex_ls {
    site local-hcc {
        pfn "file:///ProkEvo_dir/scripts/ls.sh"
    }
}

tr ex_generate {
    site local {
        pfn "file:///ProkEvo_dir/sub-dax.py"
    }
}