Fix and improve tests for genome and assembly submission workflows

[ochkalova]

Description of the bug

Currently pipeline lacks good testing with lots of test cases. 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

[ochkalova]

What tests were done:

Mode mags

1. [test_mag_complete_metadata] Single MAG with complete metadata; validates standard happy-path submission.
2. [test_mag_no_coverage_single_reads] Single MAG with missing genome_coverage and single-end reads; validates coverage estimation from one FASTQ.
3. [test_mag_no_coverage_paired_reads] Single MAG with missing genome_coverage and paired-end reads; validates coverage estimation from paired FASTQs.
4. [test_mag_no_quality] Single MAG with missing completeness and contamination; validates quality metrics backfill path. Note: this tests requires CheckM2 DB that can't be downsized for tests due to Allow relaxing of checksum check on database to allow small test database chklovski/CheckM2#140. Therefor this test is only ment to be executed occasionally on a machine with decent amount of RAM (30 Gb+)
5. [test_mag_no_taxonomy] Single MAG with missing NCBI_lineage; runs CAT_pack using small test DB.
6. [test_mag_one_contig] Single MAG with one-contig assembly; validates validation + filtering of one contig assemblies.
7. [test_mag_multiple_bins_missing_metadata] Multi-bin MAG input with mixed missing metadata (genome_coverage, RNA_presence, NCBI_lineage); validates mixed branching in one run.
8. [test_mag_register_study] No --submission-study is given as input, it has to be created during pipeline run

Mode metagenomic_assemblies

1. [test_assembly_complete_metadata] Single assembly with complete metadata; validates standard happy-path submission.
2. [test_assembly_no_coverage_paired_reads] Assembly with missing coverage and paired-end reads; validates coverage calculation path for assemblies.
3. [test_assembly_no_coverage_single_reads] Assembly with missing coverage and single-end reads
4. [test_assembly_one_contig] Assembly with one-contig FASTA; validates one-contig edge-case behavior for assembly submission.
5. [test_assembly_register_study] No --submission-study is given as input, it has to be created during pipeline run

TODO:

Mode metagenomic_assemblies

1. [test_assembly_multiple_missing_metadata] Multi-assembly input with mixed missing metadata

Test organisation

Figure out what should be defined in test_full.config and test.config

"Missing secrets" error emerging on GitHub CI that causes all nf-tests to fail.

[ochkalova]

Resolved in #39