A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

:x: *mhcquant/test_full* failed :crying_cat_face: *Run Name*
loving_fermat *Duration*
21m 47s *Status*
:x: Failed *Error Message*
```(more omitted..)
2026-10-08 08:40:45,279 INFO Adding MS²PIP-derived features to PSMs.
2026-10-08 08:40:45,362 INFO Running MS²PIP for PSMs from run (1/3) `PBMC007_msms31`...
2026-10-08 08:40:46,800 INFO Downloading model_20210316_Immuno_HCD_B.xgboost to null/model_20210316_Immuno_HCD_B.xgboost...
2026-10-08 08:42:12,607 INFO Downloading model_20210316_Immuno_HCD_Y.xgboost to null/model_20210316_Immuno_HCD_Y.xgboost...
Traceback (most recent call last):
  File "/usr/local/bin/ms2rescore_cli.py", line 177, in &lt;module&gt;
    sys.exit(main())
             ^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1442, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1363, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 794, in invoke
    return callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/bin/ms2rescore_cli.py", line 173, in main
    rescore_idxml(kwargs["psm_file"], kwargs["output_path"], config)
  File "/usr/local/bin/ms2rescore_cli.py", line 84, in rescore_idxml
    rescore(config, psm_list, )
  File "/usr/local/lib/python3.12/site-packages/ms2rescore/core.py", line 79, in rescore
    fgen.add_features(psm_list)
  File "/usr/local/lib/python3.12/site-packages/ms2rescore/feature_generators/ms2pip.py", line 194, in add_features
    ms2pip_results = correlate(
                     ^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/ms2pip/core.py", line 275, in correlate
    ms2pip_parallelized = _Parallelized(
                          ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/ms2pip/core.py", line 544, in __init__
    v...``` *Command Line*
```nextflow run '<https://github.com/nf-core/mhcquant>' -name loving_fermat -params-file '<https://api.cloud.seqera.io/ephemeral/ZIBSkAbNxxGlfhUp8brHAQ.json>' -with-tower -r dev -profile test_full``` Oct 8, 2026 at 8:44 AM

<@UPC8CHDKQ> why is test full running multiple times here? You debugging aws automation with <#CE9BJ6X6V>? :smile:

correct, your approval for the patch PR kicked off a run :slightly_smiling_face:

Ahh makes sense, Not sure why this error was thrown, previous 3.3.0 was fine

<https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3yBKOTOEyIw3i2/logs> looks like a zenodo problem/throttle