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uclahs-cds / pipeline-call-NonCanonicalPeptide

Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
https://automatic-adventure-o4l96o9.pages.github.io/
GNU General Public License v2.0
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README to add #27

Closed lydiayliu closed 2 years ago

lydiayliu commented 2 years ago
  1. in https://github.com/uclahs-cds/pipeline-call-NonCanonicalPeptide#config add decoyFasta and encodeFasta
lydiayliu commented 2 years ago
  1. filter_fasta should be removed from the README params as it no longer does anything?

    | filter_fasta | no | Whether to run filterFasta on the variant peptide FASTA called by callVariant. Defaults to false. |

Filtering now seems to be controled by the presence and absence of the blocks in filterFasta

zhuchcn commented 2 years ago
  1. filter_fasta should be removed from the README params as it no longer does anything?

| filter_fasta | no | Whether to run filterFasta on the variant peptide FASTA called by callVariant. Defaults to false. |

Filtering now seems to be controled by the presence and absence of the blocks in filterFasta

Yes! Will fix this to my next PR. Please reminder me if I don't!