Subworkflow for coverage calculations

[evanroyrees]

Wanted

Subworkflow to perform read alignments and coverage calculations.

Required

multiple channels emitting file formats to be used by their respective tool.

For reference, coverage file formats are being discussed here: (issue-#5)

File formats to emit

• alignments.sam
• alignments.bam
• coverage.tsv (header with at least contig and coverage columns)
• coverage.tsv (no header)

[chasemc]

nf-core has bowtie module, but they changed their format.

Old format still here:
https://github.com/KwanLab/Autometa/tree/dev/modules/nf-core/modules/bowtie2/align