Mitohifi fix

[SaimMomin12]

Based on the issue reported #1454 the current PR deals with adding of an additional parameter -a to the mitohifi tool for organism selection

[SaimMomin12]

It looks like I might need to fix the older tests of the tool. Converting this PR to draft until all the tests have been fixed.

[bgruening]

Dataset metadata verification for [file_ext] failed, expected [fasta] but found [txt]. Dataset API value was [{'model_class': 'HistoryDatasetAssociation', 'id': '56a37e5219746e29', 'name': 'MitoHiFi on data 4, data 3, and others: contigs circularization', 'history_id': '8efea023adb3383e', 'hid': 10, 'deleted': False, 'visible': True, 'type_id': 'dataset-56a37e5219746e29', 'type': 'file', 'create_time': '2024-07-18T09:45:56.226666', 'update_time': '2024-07-18T09:48:55.132635', 'url': '/api/histories/8efea023adb3383e/contents/56a37e5219746e29', 'tags': [], 'history_content_type': 'dataset', 'copied_from_ldda_id': None, 'dataset_id': '56a37e5219746e29', 'state': 'ok', 'extension': 'txt', 'purged': False, 'genome_build': '?', 'hda_ldda': 'hda', 'accessible': True, 'misc_info': '2024-07-18 09:45:57 [INFO] Welcome to MitoHifi v2. Starting pipeline...\n2024-07-18 09:45:57 [INFO] Length of related mitogenome is: 15354 bp\n2024-07-18 09:45:57 [INFO] Number of genes on related mitogenome: 37\n2024-07-18 09:45:57 [INFO] Running MitoHifi', 'misc_blurb': '2 lines', 'file_ext': 'txt', 'file_size': 55, 'resubmitted': False, 'meta_files': [], 'data_type': 'galaxy.datatypes.data.Text', 'peek': '

ptg000001l\t(True, 0, 14917)

ptg000001l\t(False, -1, -1)

', 'creating_job': '0c82b0d9d73436db', 'rerunnable': True, 'uuid': '36c0a844-a1a9-4a40-9548-f261237aabc8', 'permissions': {'manage': ['56e0507747f72083'], 'access': []}, 'file_name': '/tmp/tmp7xey_924/files/3/6/c/dataset_36c0a844-a1a9-4a40-9548-f261237aabc8.dat', 'display_apps': [], 'display_types': [], 'validated_state': 'unknown', 'validated_state_message': None, 'annotation': None, 'download_url': '/api/histories/8efea023adb3383e/contents/56a37e5219746e29/display', 'api_type': 'file', 'created_from_basename': 'all_contigs.circularisationCheck.txt', 'hashes': [], 'drs_id': 'hda-59f456db49caf537', 'sources': [], 'object_store_id': None, 'quota_source_label': None, 'metadata_dbkey': '?', 'metadata_data_lines': 2}].

[SaimMomin12]

For the failing test no 8, I think we might need to update our docker image to the latest one. This is available here. This should most probably fix the issue. @bgruening could you please also have a look at this?

[bgruening]

What version is that?

[bgruening]

Or better what version should the container have?

[SaimMomin12]

@bgruening The latest version of the tool is v3.2.2 realeased in March'24

[Hymenium]

Not sure what the error message are for the failed tests, but these seem to differ from similar tests by asking for circularization.

[SaimMomin12]

@Hymenium Not sure whats going wrong - The expected files from one of the failing test is gbk.HiFiMapped.bam.filtered.assembled.a_ctg.fa which is missing from the expected outputs.

[Hymenium]

I can't see this file name in the outputs mentioned in the MitoHiFi ReadMe.

It says if the flag '-r' is used then an important output is 'gbk.HiFiMapped.bam.filtered.fasta', which seem to have a similar name. Although there is no assembly, which seem to happen in the file 'hifiasm.contigs.fasta'.