Enhance run_comebin.sh and gen_cov_file.sh

[tnmquann]

Hi @ziyewang,

I've made some modifications to the bash scripts run_comebin.sh and gen_cov_file.sh for better handling compressed files. I also add some improvements to make input and output handling more flexible, allowing the use of compressed files, regex expressions, and direct file references.

Feel free to review and update them as needed. I have tested the revised scripts, and they run stably on my cluster.

bash /COMEBin/COMEBin/scripts/gen_cov_file.sh \
    -a ${contig_file} \
    -o . \
    -f ${reads_1} \
    -r ${reads_2} \
    -t ${params.thread_num}

bash /COMEBin/COMEBin/run_comebin.sh \
    -a ${contig_file} \
    -o "\$INIT_DIR/${contig_name}_binning" \
    -p ${bam_file} \
    -t ${params.comebin_thread_num}

[jolespin]

@tnmquann any chance these updates relax the dependency constraints?

[tnmquann]

@tnmquann any chance these updates relax the dependency constraints?

Yes, the updates partly relax the constraints by allowing more flexible input handling (e.g., compressed files and regex-based file targeting), but they don’t modify COMEBin core dependencies. I'm currently still using the two modified bash scripts mentioned above, and the results remain consistent - no impact on output or performance observed so far.

[jolespin]

When I get some time, I'll try to fork yours so I can decrease the dependency restrictions.

@ziyewang are you still actively developing this software?