Comments (5)
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
from checkatlas.
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.
from checkatlas.
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 !
from checkatlas.
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.
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Alright ! I will do that !
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Related Issues (20)
- QC figures does not display parameters for Seurat object
- Parse additional cellranger outputs HOT 3
- Add knee plots HOT 5
- Add Muon object
- Seurat import HOT 1
- Checkatlas conda, docker, singularity definition file HOT 2
- Dim reduction metric management for seurat object
- Integration to scVerse
- Improve Mito and ribo QC calculation
- Implement metrics from Malte Luecken's integration benchmark
- Dimensionality reduction metrics
- Add SpatialData management
- Add multiomic singlce cell mangamenet
- Create github with all metrics
- Add test datasets
- Tutorial for adding metrics in checklatlas
- Spatial Image QC
- Add test datasets for spatial transcriptomics
- Implement metrics from Antoine Collin master thesis
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