Failed parallel singularity pulls

[rsuchecki]

First run of the workflow (e.g. new system or user) with singularity involves pulling multiple container images from docker hub. This can fail likely due to race conditions in singularity.

nextflow-io/nextflow#1210
sylabs/singularity#3634

Until that is fixed a separate script could be used to pull all the containers sequentially prior to main workflow execution.

[rsuchecki]

Run once to pull (most of) the images sequentially if encountering this issue

nextflow run csiro-crop-informatics/biokanga-manuscript/pull_containers.nf

[rsuchecki]

Updated Singularity issue https://github.com/sylabs/singularity/issues/5020 with a fix in the upcoming release (3.6)

[rsuchecki]

Based on a failed GitHub Actions run (for a77bb96) I don't think this has been fixed in singularity 3.6