ERROR ~ No such variable: top_hit

[tpall]

Description of the bug

DRAM2 test run ends with a missing variable error

nextflow run DRAM -r dev --input_fasta ../test_data/DRAM_test_data/ --outdir DRAM-test-data-call-annotate-distill --threads 8 --call --rename --annotate --use_uniref --use_merops --use_viral --use_pfam --use_camper --use_kofam --use_dbcan --use_methyl --use_canthyd --use_vog --use_fegenie --use_sulfur --distill_topic default --distill_ecosystem 'eng_sys ag' --distill_custom test-data/custom-test-distilalte.tsv -profile docker -with-report -with-trace -with-timeline

 N E X T F L O W   ~  version 25.10.0

Launching `https://github.com/WrightonLabCSU/DRAM` [astonishing_marconi] DSL2 - revision: 78dfa5926c [dev]

ERROR ~ No such variable: top_hit

System information

• DRAMv2 78dfa59 [dev]
• N E X T F L O W ~ version 25.10.0
• Desktop
• Local
• Docker
• macOS 15.7.2

Command used and terminal output

nextflow run DRAM -r dev --input_fasta ../test_data/DRAM_test_data/ --outdir DRAM-test-data-call-annotate-distill --threads 8 --call --rename --annotate --use_uniref --use_merops --use_viral --use_pfam --use_camper --use_kofam --use_dbcan --use_methyl --use_canthyd --use_vog --use_fegenie --use_sulfur --distill_topic default --distill_ecosystem 'eng_sys ag' --distill_custom test-data/custom-test-distilalte.tsv -profile docker -with-report -with-trace -with-timeline

Relevant files

No response

[madeline-scyphers]

Thanks for this. Fixed in #467 Also, you should do comma seperated with your ecosystem sheets. We are also changing the api to --summarize instead of distill, which will run all topic distill sheets, and then you can add ecosystem sheets with still --distill_ecosystem, but are moving to --sum_ecos instead. Also you can do -profile full_mode to run annotate with all normal DBs, summarize, and visualize mode. (-profile docker,full_mode in your case probably). Which is a lot shorter. So you could do

nextflow run DRAM -r dev --input_fasta ../test_data/DRAM_test_data/ --outdir DRAM-test-data-call-annotate-distill --threads 8 --rename --sum_ecos 'eng_sys,ag' --distill_custom test-data/custom-test-distilalte.tsv -profile docker,full_mode -with-report -with-trace -with-timeline

as a bit shorter of a command. We are still in the middle of changing API, so we don't have a new way to do the distill_custom new way yet. Also all the old ways still work.