fastq files not found

[dfornika]

On v1.3.0, the pipeline fails to find fastq files when launched using our helper script:

The script uses the PWD environment variable to get the name of the current working directory, and use that to find the directory containing the fastq files:

https://github.com/BCCDC-PHL/covid19.analysis-helper-scripts/blob/fc07e5753d980e3fbc5754dedaf9685fb6e2401b/scripts/run-ncov2019-artic-nf-1.3#L34

This has worked on all previous versions of the helper script, but is now giving an error message:

Please supply a directory containing fastqs or CRAMs with --directory. Specify --cram if supplying a CRAMs directory

[dfornika]

There was a change to the upstream repo on Sept. 24 related to how fastq files were found, which might be related to this issue:

connor-lab@9267579

That change has not been incorporated into this repo.

[dfornika]

We've mitigated this issue by re-arranging the order of command-line arguments:

https://github.com/BCCDC-PHL/covid19.analysis-helper-scripts/commit/15f32f3b9da59ddc8e0c2ca12d9337c8c29916ff

I'm going to leave this issue open because I'd prefer to find a better solution.