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nf-core / metapep

From metagenomes to epitopes and beyond
https://nf-co.re/metapep
MIT License
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Peptide lengths can only be set over all alleles #74

Closed tillenglert closed 1 year ago

tillenglert commented 1 year ago

Description of the bug

The peptide lengths are set generally over all allele models.

As the methods do not always support all models, it may happen (e.g. in test_mouse), that one model supports peptide lengths 8, 9 in syfpeithi (H2-Db) and the other model only supports (H2-Ld). Therefore either we drop all non supported combinations during epitopeprediction or we only allow a smaller set of predictions. Another approach would be to let the user set the peptide lengths within the samplesheet and introduce a new column (Peptide_Lengths) in which the user defines either [8,9,10,11,12] or [8,12].

Command used and terminal output

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Relevant files

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System information

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tillenglert commented 1 year ago

PR #75 partially solves this. Still the user is not informed, except he looks into the prediction work directories and looks at stderr.log.