Fix file() issues for S3 outputs

[olgabot]

Updates/changes to kmermaid to make it amenable to running on many bams, not just .tar.gz files.

PR checklist

• [ ] PR is to dev rather than master
• [ ] 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 necessary, also make a PR on the nf-core/kmermaid branch on the nf-core/test-datasets repo
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
• [ ] Make sure your code lints (nf-core lint .).
• [ ] Documentation in docs is updated
• [ ] CHANGELOG.md is updated
• [ ] README.md is updated

Learn more about contributing: https://github.com/nf-core/kmermaid/tree/master/.github/CONTRIBUTING.md

[pranathivemuri]

I don't see how the changes you made

1. enabled nextflow tower
2. working on many bams
3. did you mean tenx_gz files?

[olgabot]

Hmm I think these changes are getting rid of the single bam2fasta run which used single_ksize and then changed new File to file so it can run on S3 more seamlessly. Without file, then a local folder called s3/path/to/outdir gets made and the pipeline output doesn't get saved

[olgabot]

I don't see how the changes you made

1. enabled nextflow tower

I think I meant s3 instead.. sorry

2. working on many bams

I think I meant the if params.bam section which errors out if you don't provide those other paramters

3. did you mean tenx_gz files?

This is the .tar.gz files that are output by our implementation of the cellranger count pipeline for counting reads per cell from the 10X genomics output