Update generate protein fasta and create peptide ordering form commands to use transcripts.fa - #1453
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susannasiebert wants to merge 5 commits into
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Update generate protein fasta and create peptide ordering form commands to use transcripts.fa#1453susannasiebert wants to merge 5 commits into
susannasiebert wants to merge 5 commits into
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…le instead of recreating it from original input data
…te generate protein fasta command docs
tmooney
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Aug 24, 2026
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Does this file need to exist? Might be a candidate for removal and inclusion in .gitignore.
susannasiebert
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Aug 31, 2026
Co-authored-by: Thomas B. Mooney <mooney@wustl.edu> Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>
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Currently, the generate protein fasta and create peptide ordering form commands use the same inputs as the main pipeline and regenerate the transcripts.fa file from it. This can lead to confusion because the same parameters used in the original runs (e.g. --pass-only, --allow-incomplete-transcripts, --biotypes) need to be applied in these command in order for the indexes to be consistent (which are used for matching entries between the VCF and the aggregated report).
This PR updates these two commands to instead use the transcripts.fa files from the original runs as the input. This file was already created using the above flags/filters so the indexes will be consistent.
This PR also adds a new standalone command
generate_transcripts_fasta. This command generates the transcripts.fa. This is mostly useful for folks that used the generate protein fasta command without an accompanying pipeline run. This new command can now be used to generate the transcripts.fa for input to the updated generate protein fasta command.TODO: