merge bwamem_index and remove unneeded multiqc options

[tkchafin]

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [ ] Make sure your code lints (nf-core lint).
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• [ ] Usage Documentation in docs/usage.md is updated.
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[tkchafin]

@reichan1998 Good catch on the -resume issue! I think I have figured it out and fixed the issue. The problem was caused by special characters in the file names for the hic and illumina samples, and the fact that I was loading meta.file as a file-path object (nextflow.file.http.XPath) and not a string. These special characters must be dealt with in some hidden way during caching which was causing the join operation to fail (i.e., the file object created from the original file and the one created from the cached file were not identical). So... after a few hours of banging my head against this, the problem was fixed by simply changing the type of meta.file defines in assets/schema_input.json:

            "datafile": {
                "format": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Data file for reads cannot contain spaces and must have extension 'cram', 'bam', '.fq.gz' or '.fastq.gz'",
                "meta": ["datafile"]
            },

Can you give it a try and see if the latest commits fix the problem?

[reichan1998]

Thank you for letting me know. It's great to hear that you have solved this problem @tkchafin ^^ I will try and get back to you later.

[reichan1998]

Hi @tkchafin, I have checked and your solution can fix the-resume issue. Happy weekend!

[tkchafin]

Thanks Weiwen! Can you click the "approve" button in the review so I can merge?

[reichan1998]

I have already approved. Thank you, Tyler!

[tkchafin]

Thanks for your review!