Fix eventual ampcombi_parsetables crash
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- Dominant language
- Nextflow
- Stars
- 119
- Forks
- 40
- Avg merge
- 2d 17h
- Merged PRs (30d)
- 5
Description
Description of feature
In some cases, ampcombi_parsetables crashes when using certain DRAMP database version. Unfortunately, the versions cannot be tracked because the maintainers simply don't provide them, only the current version. So it's hard to debug if the provided DRAMP version is the culprit.
Observed behaviour
The error message looks like this:
Traceback (most recent call last):
File "/usr/local/bin/ampcombi", line 10, in <module>
sys.exit(main())
^^^^^^
File "/usr/local/bin/ampcombi.py", line 492, in main
args.func(args) # call the default function
^^^^^^^^^^^^^^^
File "/usr/local/bin/ampcombi.py", line 467, in parse_table_log
log_output('Ampcombi_parse_tables.log', args, parse_tables)
File "/usr/local/bin/ampcombi.py", line 453, in log_output
func(args)
File "/usr/local/bin/ampcombi.py", line 258, in parse_tables
process_sample(
File "/usr/local/bin/ampcombi.py", line 323, in process_sample
sample_summary_df = pd.merge(summary_df_filtered, mmseqs_df, left_on='contig_id', right_on='query', how='left')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 110, in merge
op = _MergeOperation(
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 645, in __init__
_right = _validate_operand(right)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/core/reshape/merge.py", line 2426, in _validate_operand
raise TypeError(
TypeError: Can only merge Series or DataFrame objects, a <class 'NoneType'> was passed
Proposed solution
Upload a working DRAMP version to nf-core/testdatasets or Zenodo and use that as pipeline default. Users can then always provide their own up-to-date ones, but have a fallback solution if the current version is faulty.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in ampcombi.py at parse_tables and process_sample, especially the pandas merge that receives None instead of a DataFrame. Reproduce the crash with the affected DRAMP input and determine how the pipeline should use a working DRAMP version as its default. Done means ampcombi_parsetables no longer crashes with the provided default dataset.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100