# meta-omics oct 2024 hackathon

## What

Two day online hackathon event

### Aim

Add functionality to all primary meta-omics pipelines to auto-generate input samplesheets for each other and downstream pipelines.

### Objectives

1. Discuss, plan, and build consensus on a common system for samplesheet auto-generation
2. Implement in pipelines, with minimum of each pipeline supporting one other pipeline
3. Document usage with tutorials

## Who

Day one of the event will be aimed at primarily developers and those with Nextflow coding experience.

Day two will ideally be users who are willing to write documentation and short tutorials in tandem with the lead developers. These users _do not_ require coding experience, but should be familiar with standard bioinformatic tool documentaiton and tutorials.

## How

I propose a two day event, first day is mostly aimed at developers to actually work out how to get the common system to work and implemented in dev branches and reviewed, and then the second day for documentation and (minor) releases.

Implementation will require an initial general round table discussion by developers and coders to discuss options, then likely splitting into a smaller groups to write the code. We will then reconvene to discuss progress and address any issues that have developed. Once all is good, we will swap reviews.

Documentation will likely consist of user-developer pairs, and will first integrate typical usage documentation on how to use the new functionality. Then more specific (short) tutorials should be written by the users to give more accessible understanding by readers how such functionality can be included in their workflows.

Potential pipeline team suggestions:

| Producing pipeline | Recieving Pipeline |
|--------------------|------------------------|
| detaxizer | taxprofiler |
| taxprofiler | mag |
| mag | funcscan |
| mag | phageannotator |
| detaxizer | mag |
| mag | magmap |
| magmap | differentialabundance |
| taxprofiler | differentialabbundance |
| mag | taxprofiler |

## When

TBC, based on when2meet poll, which will be for Week 2 and Week 3 of October.

It will be best for developers to attend across both days, users/documentation writers just the second day.

We can discuss whether to allow a gap in the middle of the event so any problems can be independently solved.

No-one will be expected to attend the entire days, but ideally commit to working with others on gather.town while working on the task (not alone).

## Where

Ideally gather.town for group-splitting-off tasks

- If less than 10 people all fine
- If more, could consider asking nextflow ambassador microgrant?

Backup - Zoom plus break out rooms

## Technical notes

Example implementations

- FetchNGS module: https://github.com/nf-core/fetchngs/blob/master/modules/local/sra_to_samplesheet/main.nf
- Mahesh's in code-example: https://nextflow.slack.com/archives/C02T98A23U7/p1713258642201479?thread_ts=1713256084.608799&cid=C02T98A23U7
- Carson's subworkflow method: https://github.com/nf-core/mag/blob/5b37df5ecd80b2684298eddd496caa3c303bf02a/subworkflows/local/generate_downstream_samplesheet.nf

Things to consider:

- Probably best to not have a standalone module for this (very little to no computation)
- Need to be mindful of file paths within Nextflow channels will point to work directories rather than `--outdir` files