[Tiptoft] Deprecate Tiptoft

[MrTheronJ]

This PR closes #467
Closing all issues related to Tiptoft as they are no longer applicable.

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

Completely deprecate Tiptoft. Removes all mentions of Tiptoft from all tasks, workflows, and documentations.

⚡ Impacted Workflows/Tasks

• tasks/gene_typing/plasmid_detection/task_tiptoft.wdl
• tasks/utilities/data_export/task_broad_terra_tools.wdl
• workflows/utilities/wf_read_QC_trim_ont.wdl
• workflows/theiaprok/wf_theiaprok_ont.wdl

This PR may lead to different results in pre-existing outputs: Yes

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

Tiptoft serves as a wrapper for an outdated version of Plasmidfinder. As it is no longer maintained and duplicates the functionality of Plasmidfinder, it is no longer necessary to keep it. In contrast, our version of Plasmidfinder is actively maintained, with its databases updated continuously.

• Removed the task_tiptoft.wdl file and any reference to it.
• Removed all input/output variables referencing Tiptoft across all tasks and workflows.
• Removed all sections of documentation referencing Tiptoft.

⚙️ Algorithm

Not applicable as Tiptoft will no longer exist in PHB.

➡️ Inputs

The following inputs have been removed from the TheiaProk_ONT_PHB Workflow:

Int? tiptoft_cpu
Int? tiptoft_disk_size
String? tiptoft_docker
Int? tiptoft_memory
Int? tiptoft_kmer_size
Int? tiptoft_max_gap
Int? tiptoft_margin
Int? tiptoft_min_block_size
Int? tiptoft_min_fasta_hits
Int? tiptoft_min_kmers_for_onex_pass
Int? tiptoft_min_perc_coverage

⬅️ Outputs

The following outputs have been removed from TheiaProk_ONT_PHB Workflow:

File? tiptoft_plasmid_replicon_fastq
String? tiptoft_plasmid_replicon_genes
String? tiptoft_version

🧪 Testing

Tested ONT samples with known plasmids with and without Tiptoft present.

TheiaProk_ONT_PHB with Tiptoft ~ 4 samples
TheiaProk_ONT_PHB without Tiptoft ~ 4 samples
TheiaProk_ONT_PHB ~ 44 validation samples

Additionally, Plasmidfinder identified the same plasmids from the TheiProk_ONT_PHB workflow, regardless of whether Tiptoft was included or not.

• plasmidfinder_plasmids without Tiptoft:

ERR8958719 (theiaprok_ont) : "Col440I,IncFIB(K),IncFIB(pQil),IncFII(K),IncFII(K),IncFII(K),IncR"
ERR8958833 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"
ERR8958837 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"
ERR8958851 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"

• plasmidfinder_plasmids with Tiptoft:

ERR8958719 (theiaprok_ont) : "Col440I,IncFIB(K),IncFIB(pQil),IncFII(K),IncFII(K),IncFII(K),IncR"
ERR8958833 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"
ERR8958837 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"
ERR8958851 (theiaprok_ont) : "rep16,rep16,rep19,rep22,rep5a"

Suggested Scenarios for Reviewer to Test

The TheiaProk_ONT workflow has only been tested with 4 ONT samples (with plasmids). It might be beneficial to test with additional ONT data known to contain plasmids.

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable
  • You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three workflows_overview tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated