Matthieu Muffato

The plan looks great, @ewels 👍🏼

Today, with @DLBPointon, we talked about making the path to the painting database table (the tsv file) a parameter of the pipeline. The databases shouldn't be stored in the repository...

> Currently the reference file is stored in the assets of the treeval pipeline, now 2 pipelines are using it. We need to start storing these on S3. Internally we...

That would be great, thank you !

I got this error in `UPLOAD_HIGLASS_DATA` when running the full test: ``` Command error: W1009 12:03:04.412509 41 loader.go:222] Config not found: /nfs/users/nfs_m/mm49/.kube/config.tol-it-dev-k8s W1009 12:03:04.450610 96 loader.go:222] Config not found: /nfs/users/nfs_m/mm49/.kube/config.tol-it-dev-k8s...

Dear @krishn-cpu . I have to say this is a strange pull-request. I know you left some comments on two issues, but the PR here should still have a description...

HI @DLBPointon . I'm having an issue when running the pipeline. It can't find the Singularity image: ``` ERROR ~ Error executing process > 'SANGERTOL_GENOMENOTE:GENOMENOTE:ANNOTATION_ANCESTRAL:ANCESTRAL_PLOT (1)' Caused by: Failed to...

So far the Singularity URLs I've seen are very different from the Docker ones, cf https://github.com/sanger-tol/genomenote/blob/main/modules/nf-core/samtools/view/main.nf#L7-L8 `community.wave.seqera.io/library/r-optparse_r-scales_r-tidyverse:9b4155b6beecffd1` is valid for Docker containers, and for Singularity as long as it's just...

> One issue I've noticed on the runner though is that the ENA requests fail when both test pipelines are running at the same time. Hopefully this is temporary or...

Yes, in another PR. `if (note_template) {`: possibly, but I can see in the workflow file that `GENOME_METADATA.out` is used for the `COMBINE_NOTE_DATA` subworkflow, which is essentially using `ch_note_template` to...