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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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Not possible to set `verbose-level` for `callVariant` #84

Closed lydiayliu closed 1 year ago

lydiayliu commented 1 year ago

Current params supported https://github.com/uclahs-cds/pipeline-call-NonCanonicalPeptide/blob/37ffb75ed403352ad79496b3001c80de09497073/modules/call_variant.nf#LL4-L16C2

Quite a few has been added since then

usage: moPopGen [-h] [-V] <command> [options] callVariant [-h] -i ['<files>'] [['<files>'] ...] -o <file> [--max-variants-per-node <number>]                                 
                                                          [--additional-variants-per-misc <number>] [--min-nodes-to-collapse <number>] [--naa-to-collapse <number>]          
                                                          [--noncanonical-transcripts] [--verbose-level <number>] [--threads <number>] [-g <file>] [-a <file>]               
                                                          [--reference-source {gencode,ensembl}] [-p <file>] [--invalid-protein-as-noncoding] [--index-dir [<file>]]         
                                                          [-c <value>] [-m <number>] [-w <number>] [-l <number>] [-x <number>] [-q]