I finally figured out why I couldn't run Pharmcat from the output created by the pipeline. The last line of run.sh was deleted in an old commit, so no usable file was created.
also, the file that the line references was also deleted in the same commit:
pgkb-ngs-pipeline/external_data/grc38_pgx.tight.list
For anyone else coming across this issue, you can manually enter this line back and replace the .tight.list file in that directory and then pharmcat will run.
I finally figured out why I couldn't run Pharmcat from the output created by the pipeline. The last line of run.sh was deleted in an old commit, so no usable file was created.
https://github.com/PharmGKB/pgkb-ngs-pipeline/commit/02966ce25cfcb60550d561d7cc106f1753bd6b58#diff-1b0c2b516b83393edb7200ad5ff12181L114
also, the file that the line references was also deleted in the same commit: pgkb-ngs-pipeline/external_data/grc38_pgx.tight.list
For anyone else coming across this issue, you can manually enter this line back and replace the .tight.list file in that directory and then pharmcat will run.