Fix and improve tests for genome and assembly submission workflows #32
Description
Description of the bug
Currently pipeline lacks good testing with lots of test cases. The other issue that have to be fixed is "Missing secrets" error emerging on GitHub CI that causes all nf-tests to fail. Finally, test configs have be reorganised and improved.
Minimal list of test cases to be checked and implemented:
--mode bins or mags:
- coverage, completeness, contamination, RNA and taxonomy are provided, submission_study is set - successful submission
- coverage, completeness, contamination, RNA and taxonomy are NOT provided, submission_study is set - successful submission
- submission_study is NOT set - successful submission
--mode metagenomic_assemblies:
- coverage is provided, submission_study is set - successful submission
- coverage is NOT provided, reads are single, submission_study is set - successful submission
- coverage is NOT provided, reads are paired, submission_study is set - successful submission
- assembly has 1 contig - unsuccessful submission
- submission_study is NOT set - successful submission
Command used and terminal output
Relevant files
No response
System information
No response