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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`decoyFasta` unrecognized arguments #24

Closed lydiayliu closed 2 years ago

lydiayliu commented 2 years ago
      set -euo pipefail

      moPepGen decoyFasta \
          --input-path ACH-000083_mutation-Noncoding_encoded.fasta \
          --output-path ACH-000083_mutation-Noncoding_encoded_decoy.fasta \
           --decoy-string-position prefix --decoy-string DECOY_

    Command exit status:
      2

    Command output:
      (empty)

    Command error:
      usage: moPopGen [-h] [-V] <command> [options]
      moPopGen: error: unrecognized arguments: --decoy-string-position prefix

Seems like mpg has mixed use of - and _, we should standardize

Decoy Database Parameters:
  --decoy-string <value>                                                                                                                                                    
                        The decoy string that is combined with the FASTA header for decoy sequences. (default: DECOY_)
  --decoy_string_position <value>                                                                                                                                           
                        Should the decoy string be placed at the start or end of FASTA headers? (default: prefix)