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openpipelines-bio / openpipeline

https://openpipelines.bio
MIT License
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[BUG] Path of inner enrichment primers is not converted to absolute path for processing #716

Closed ddemaeyer closed 2 months ago

ddemaeyer commented 2 months ago

https://github.com/openpipelines-bio/openpipeline/blob/5f226595856eb9957727a030f1e65efbf14d05fe/src/mapping/cellranger_multi/script.py#L94

Running the inner enrichments results in: 

 Log message:
  The file specifying inner enrichment primers (_viash_par/vdj_inner_enrichment_primers_1/cs000251-vdj-t-gd-primers.txt) does not exist or is not readable. Please check the path on machine nf-fe6c777f40c9932486e814ff20f40d20-k4w9q.