Fix Dockerfile for multiqc vs new python

[marcodelapierre]

No description provided.

[pditommaso]

Interesting, wonder if wave --conda-package multiqc=1.17 works of if it's broken as well

[emi80]

@pditommaso, indeed wave --conda-package multiqc=1.17 works as I have been using that version in my tests with Singularity 4

[marcodelapierre]

interesting! below is what I needed for it to work:

• python < 3.12
• typing_extensions
• importlib_metadata

FROM mambaorg/micromamba
MAINTAINER Paolo Di Tommaso <[email protected]>

RUN \
   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
      salmon=1.10.2 \
      fastqc=0.12.1 \
      multiqc=1.17 \
      python=3.11 \
      typing_extensions \
      importlib_metadata \
      procps-ng \
   && micromamba clean -a -y

ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER root

[marcodelapierre]

CI fails due to current image on quay.io:

In https://github.com/nextflow-io/rnaseq-nf/actions/runs/6770165713/workflow?pr=23:

    - name: Tests
        run: |
          curl -fsSL get.nextflow.io | bash
          ./nextflow run . -profile docker
        env:
          NXF_ANSI_LOG: false

In nextflow.config:

  docker {
    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
    docker.enabled = true
  }

[pditommaso]

Think I need to rebuild the container, let me try

[pditommaso]

Should be ok

[marcodelapierre]

yep