A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Or better still, don't use a custom container at all and grab one from biocontainers or Seqera Containers..

This was previously impossible due to the environment specs, but we will try this again once the environment has stabilised.

I just tried it out of curiosity, I think it worked:
```$ wave --freeze --conda-file environment.yml --await

community.wave.seqera.io/library/gcc_gxx_imagecodecs_jupyter_pruned:c5ac1d7bb15985e3```

With this conda env file:
```channels:
  - conda-forge
  - bioconda
dependencies:
  - gcc=13.2.0
  - gxx=13.2.0
  - imagecodecs=2024.1.1
  - jupyter=1.0.0
  - leidenalg=0.9.1
  - libgdal=3.8.3
  - papermill=2.3.4
  - pip=23.0.1
  - python=3.10
  - pip:
      - harmonypy==0.0.10
      - scanorama==1.7.4
      - scanpy==1.10.0
      - squidpy==1.4.1
      - scipy==1.12.0
      - spatialdata-io==0.1.5
      - spatialdata-plot==0.2.6
      - spatialdata==0.2.3```

Logs etc here: <https://wave.seqera.io/view/builds/bd-c5ac1d7bb15985e3_1>

Though this is without the customer Dockerfile, so won't have quarto etc.

(can probably just add Quarto to the environment.yml file though?)

Yes, this might be possible now; previously, installing Quarto through Conda didn't work for arm64 systems due to an issue with pandoc, but I think this might have been solved now. Christophe is currently working on adding Visium HD to the pipeline, so once that's finalised we'll see if we can use Seqera Containers for this environment (including Quarto) and change it to that, if it works