Bringing back Docker support, possibly as a replacement for the various Conda environments

[amizeranschi]

Inspired by a recent comment from @gabeng, I wanted to ask if it would be a great deal of effort to bring back Docker support and the creation of new Bcbio Docker images.

One alternative to reviving bcbio-nextgen-vm (although perhaps more laborious) could be to have the possibility to replace Conda environments with several Docker containers in bcbio-nextgen itself, as they do for example in nf-core/sarek. Given how often Conda has been breaking bcbio installs during the last couple of years, it could be worth the effort to replace it, or at least offer the possibility of using Docker containers as an alternative. And this could also pave the way for Kubernetes support at some point.

Here's a list of the Docker images currently on my system, after a few variant calling experiments with the above pipeline:

$ docker image ls
REPOSITORY                                                                 TAG                                          IMAGE ID       CREATED         SIZE
nfcore/snpeff                                                              5.1.R64-1-1                                  0462080aa43c   2 weeks ago     1.4GB
nfcore/vep                                                                 106.1.R64-1-1                                e5c98f96ae89   2 weeks ago     1.22GB
quay.io/biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb   551156018e5580fb94d44632dfafbc9c27005a0e-0   5703dbdd3100   2 weeks ago     1.01GB
quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f   3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0   c4f4a546ff1b   3 weeks ago     1.26GB
quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40   219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0   a3d569a08aa5   3 weeks ago     133MB
quay.io/biocontainers/gatk4                                                4.3.0.0--py36hdfd78af_0                      0f8cc7afc8e6   7 weeks ago     966MB
quay.io/biocontainers/bcftools                                             1.16--hfe4b78e_1                             7ec55dde74af   8 weeks ago     198MB
quay.io/biocontainers/samtools                                             1.16.1--h6899075_1                           09cd4486af55   8 weeks ago     62MB
quay.io/biocontainers/freebayes                                            1.3.6--hbfe0e7f_2                            9c664cb1521f   2 months ago    326MB
quay.io/biocontainers/tiddit                                               3.3.2--py310hc2b7f4b_0                       e9c7cf6b37d7   2 months ago    350MB
quay.io/biocontainers/multiqc                                              1.13--pyhdfd78af_0                           747595fd0a8e   2 months ago    431MB
google/deepvariant                                                         1.4.0                                        decb60cd33cb   6 months ago    5.72GB
quay.io/biocontainers/sra-tools                                            2.11.0--pl5321ha49a11a_3                     58aa27074b50   9 months ago    379MB
quay.io/biocontainers/mosdepth                                             0.3.3--hdfd78af_1                            14b81386a558   10 months ago   22.5MB
quay.io/biocontainers/fastp                                                0.23.2--h79da9fb_0                           371123966d85   12 months ago   52MB
quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a   6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0   8bb307eced25   14 months ago   387MB
quay.io/biocontainers/python                                               3.9--1                                       34c2b9e3810c   17 months ago   191MB
quay.io/biocontainers/cnvkit                                               0.9.9--pyhdfd78af_0                          65c84d95fbda   18 months ago   1.12GB
quay.io/biocontainers/tabix                                                1.11--hdfd78af_0                             171149a492ea   19 months ago   94.3MB
quay.io/biocontainers/manta                                                1.6.0--h9ee0642_1                            0be19048fb6e   20 months ago   200MB
quay.io/bcbio/bcbio-vc                                                     latest                                       196407441ba3   23 months ago   5.89GB
quay.io/biocontainers/gawk                                                 5.1.0                                        1f25a9f620a3   2 years ago     38.6MB
quay.io/biocontainers/vcftools                                             0.1.16--he513fc3_4                           edbf7b8881c0   2 years ago     48MB
quay.io/biocontainers/fastqc                                               0.11.9--0                                    9d444341a7b2   2 years ago     531MB
quay.io/biocontainers/bwa                                                  0.7.17--hed695b0_7                           5c6028c4ea33   2 years ago     109MB