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)

We need a small test data set:
Related: KwanLab/Autometa#152

We also need to decide on a common input tsv that can accommodate input data for all the tools.

See example:
https://nf-co.re/mag/2.1.0/usage#samplesheet-input-file

sample_id short_reads_1 short_reads_2 contigs ????? ????

Thoughts on moving the documentation regarding creating new metaBenchmark modules to CONTRIBUTING.md or some other document?

Maybe also a TUTORIAL.md would be good and this could be linked in the README.md?

To prepare for the Autometa v2 publication, which should reference this repo, the documentation needs to be cleaned up so that readers of that paper, and others of the community:

1. Know what this repository is, and what it is used for.
2. How to use it
3. How to add to and contribute to it.

I have not done a deep dive into this project yet, but it would also be useful to have instructions on:

4. How to get the reference data, including CAMI I and CAMI II.

https://github.com/CAMI-challenge/AMBER
https://github.com/CAMI-challenge/OPAL

• Add documentation for formatting taxonomy profiling output
• Add documentation for formatting binning output
• Add documentation for subworkflow to call tool and tool-output-formatter