Feat/irods archive

[davehorsfall]

Pull Request Template

Summary

This PR provides support for searching the team298 iRODS archive.

Fixes #44

Changes Made

• Updates imeta-report to include collection results from /archive/team298 iRODS zone.
• Updates iget-fastqs to download collection results from /archive/team298 iRODS zone.
• Changes the all-imeta-report.csv report to include the full list of actual collection paths, instead of the summary, which I think is more useful for the user.

To test use:

./solosis-cli irods imeta-report --sample SIL01
./solosis-cli irods iget-fastqs --sample SIL01

Please note, there are not actual FASTQs in the archive yet, but the collections exists and are tagged with metadata, so the Solosis commands will run and give output.

Checklist

• The code adheres to the project's style guidelines
• Documentation has been updated (if applicable)
• Tests have been added/updated (if applicable)
• I have linked this PR to an issue (if applicable)
• I have reviewed my own code for potential issues

[codecov]

Codecov Report

❌ Patch coverage is 10.00000% with 36 lines in your changes missing coverage. Please review.
✅ Project coverage is 42.86%. Comparing base (4e95895) to head (c5cd86f).
⚠️ Report is 252 commits behind head on dev.

Files with missing lines	Patch %	Lines
solosis/commands/irods/iget_fastqs.py	14.28%	24 Missing ⚠️
solosis/commands/irods/imeta_report.py	0.00%	12 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #152      +/-   ##
==========================================
- Coverage   43.58%   42.86%   -0.73%     
==========================================
  Files          28       28              
  Lines        1131     1157      +26     
==========================================
+ Hits          493      496       +3     
- Misses        638      661      +23     

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[louisegrimble]

when running
./solosis-cli irods iget-fastqs --sample SIL01

the following was the output, is this okay? it says it cannot find the temp dir with the metadata.tsv is just because you have already run this command on this sample?

ERROR: Nextflow 24.10.5 is available - Please consider updating your version to it
ERROR: Metadata TSV file /lustre/scratch126/cellgen/team298/data/tmp/d2bd00bc/metadata/metadata.tsv not found.
INFO: Looking for data in team archive






[16:39:35] Report saved to /lustre/scratch126/cellgen/team298/data/samples/SIL01/imeta_report.csv
INFO: FASTQ files for sample "SIL01" will be downloaded to: /lustre/scratch126/cellgen/team298/data/samples/SIL01/fastq
INFO: Job submitted successfully: Job <184687> is submitted to queue <small>.