CI seems broken

[cjfields]

@grbot may take this one.

There appear to be issues with CI using Github Actions which may be related to Nextflow and/or Singularity. For an example, see https://github.com/h3abionet/TADA/actions/runs/1254767934.

Note a similar issue has been reported before for nf-core workflows, see the comment (and possible solutions) in this thread:

nf-core/rnaseq#494 (comment)

[grbot]

Thanks @cjfields for the link. Did not pick it up during searching last night.

I do think however we have all that is suggested.

1. In https://github.com/h3abionet/TADA/runs/3655307193?check_suite_focus=true#step:8:2542 our version is > 20.11.0-edge . This sounds like to overall solution. Others are
2. Use a more recent Singularity (>= 3.6). Ours here: https://github.com/h3abionet/TADA/blob/master/.github/workflows/ci.yml#L46 is 3.8
3. It also seems that the --disable-cache options are not recognised with the singularity.engineOptions during the pull command (which might be a possible solution). Also do not want to have something like this customised in our CI though.

Still need to figure this out.

[cjfields]

It appears CI is working on the branches, so maybe what we can do is determine a time to merge in any changes from the dev branch (which is where I'm working on accumulating various feature additions) into master.

[cjfields]

Looks like CI is working with Docker. I'm working on reorganizing the testing on the fix-CI branch at the moment, will merge into dev.

[cjfields]

This appears to be passing on the pull request, so pulling into the dev branch (where we will consolidate feature updates that can be merged into the stable master branch for releases).