Integration with nf-core pipelines about checkatlas

[drbecavin]

Dear Gregor,

Thanks for your interest in checkatlas ! I would love to make it compatible with your two nf-core pipelines. It is actually a planned development to integrate the spatial. As we are using more and more these type of data in the lab.

You are totally right ! Nextflow should be on top of the checkatlas pipeline. I first developed checkatlas as a stand-alone python program and then added nextflow in the last months. Not being a nextflow expert, I implemented it, the fastest way i knew.

Sadly, I do not have any grant to found this project. So I am alone on the development. If you feel that checkatlas would be a great addition to your pipeline. I would love to interact with you and make it "nf-core" compatible. Some help would be more than useful !

DM me : becavin AT ipmc DOT cnrs DOT fr

[grst]

Hi @drbecavin,

I now had a chance to play around with checkatlas a bit more. I now understood that the nextflow part is optional and it also runs quite well without it.

For moving forward, we mainly need two things:

• a container, preferably lightweight and without the nextflow and R dependencies. As mentioned in #25, I recommend using bioconda for that, as it will give you conda, docker+singularity in one go. I can help with creating the bioconda recipe.
• Full MultiQC integration, i.e. getting MultiQC/MultiQC#1713 merged.

Once we have that, I would create a module on nf-core/modules that can be integrated into different pipelines.

[drbecavin]

Hello @grst

The nextflow is essentially there when you want to calculate extensive metrics for classification, annotation and dim reduction. In these cases it takes a lot of time and one need to parallelise the datasets.

Ok, next week I will work on :

• The bioconda definition
• Fix problem for MultiQC PR

I can also start a draft nextflow pipeline for the whole checkatlas run (replacing my current nextflow.nf). Which you would be able to use and improve.

I'll get you posted.
thanks !

[grst]

I can also start a draft nextflow pipeline for the whole checkatlas run (replacing my current nextflow.nf). Which you would be able to use and improve.

in that case consider starting from the nf-core template. It may seem a bit overwhelming in the beginning, but the community figured out a lot of things to make it easy to run it seamlessly across different setups. Also it makes it easier to publish it as an nf-core pipeline later.

[drbecavin]

Alright ! I will do that !