Allow relative file paths

[RamiyapriyaS]

Description

Changes allow for command line parameters to be provided as relative paths.

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

• Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

  For each relevant configuration:

  • Can the program run completely through without erroring out? Yes
  • Does it produce the expected outputs, given the inputs provided? Yes

[RamiyapriyaS]

PR Testing:

Run the pipeline with relative paths for the following parameters: meta_path, submission_config, ref_fasta_path, ref_gff_path, and bakta_db_path.

Example command:

nextflow run main.nf -profile test,singularity --species virus --annotation --submission --output_dir rjd0_rel_path --submission_config conf/submission_config.yaml --ref_fasta_path assets/ref/ref.MPXV.NC063383.v7.fasta

[jessicarowell]

Test data with --virus and --rsv is working, but --bacteria is not. I tried reversing the change to the bacteria annotation subworkflow - no change, so not sure when/how this broke.

nextflow run main.nf -profile singularity,test --species bacteria --output_dir test_alan --submission_config ~/02.scratch/submission_config.yaml --bakta_db_path /scicomp/reference/bakta/db --submission true --submission_wait_time 1 --annotation true --meta_path ~/02.scratch/bacteria_test_metadata_2.xlsx

The metadata path is a custom one where I removed the CP sample because it's giving us issues (see #217).

This is the output:

Metadata log says "Metadata validation was successful!"

[jessicarowell]

Tested --virus and --rsv with test data. Failed for me on a custom bacteria metadata file, but it worked for Ramiya with the test datasets. I'll go ahead and merge because this is probably an issue with my metadata file.