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.
02966ce#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.
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.
02966ce#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.