Updates to immuno workflow for upcoming 4.0.0 release #1085
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tmooney
reviewed
Mar 13, 2023
definitions/tools/pvacseq.cwl
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| @@ -15,14 +15,14 @@ arguments: [ | |||
| { valueFrom: " && ", shellQuote: false }, | |||
| "/usr/local/bin/pvacseq", "run", | |||
| "--iedb-install-directory", "/opt/iedb", | |||
| "--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp", | |||
| "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz", | |||
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Would it make sense for this to be an input the user could specify but with this path as the default?
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Good question. @malachig @chrisamiller do you have any opinions?
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This implements the features as discussed here: wustl-oncology/analysis-wdls#87
Still outstanding is the addition of Arriba to run in parallel to starfusion/AGfusion.