Feature/update to dbcan3#500
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Using the run_dbcan tooling, update our use of dbcan from dbcan2 to dbcan3. We will use the easysubstrate call to run the entire run_dbcan pipeline. This initial step just consumes the first stages output and does not include the CGC or easysubstrate in our annotation or summarize. Add parsing for run_dbcan output to incorporate into raw-annotations.tsv Add ability for dram to check DB version with added version file. This is an optional, per database add-on that is currently only being used with dbcan to ensure users are updated to dbcan3.
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May 10, 2026
Local pipeline run on a single OWC fasta with only --use_dbcan exposed two issues that the original dbcan2 path masked because SQL_DBCAN always populated formattedOutputchannels. 1. db_search.nf: .collect() on an empty formattedOutputchannels never emits, so COMBINE_ANNOTATIONS hung waiting for input. Switched the three input channels (fastas, genes, dbcan_output) to .toList(), which always emits a list -- matches upstream PR WrightonLabCSU#500's pattern. 2. combine_annotations.py: pd.concat([]) raises ValueError. Two cases: - annotations dir empty (no other DB enabled) -> seed combined_data with an empty DataFrame carrying just query_id and input_fasta columns. - dbcan TSVs all header-only (zero CAZyme hits in the sample) -> filter the per-fasta frames first, only concat if any non-empty remain. Verified end-to-end: nextflow run . -profile docker --call --annotate --use_dbcan against the OWC_0000 fixture (9 proteins, 0 CAZymes) now completes and produces raw-annotations.tsv with the expected gene rows. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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feat: Update dbcan to dbcan3 using run_dbcan tool
Using the run_dbcan tooling, update our use of dbcan from
dbcan2 to dbcan3. We will use the easysubstrate call to run the
entire run_dbcan pipeline. This initial step just consumes the first
stages output and does not include the CGC or easysubstrate in our
annotation or summarize.
Add parsing for run_dbcan output to incorporate into raw-annotations.tsv
Add ability for dram to check DB version with added version file. This
is an optional, per database add-on that is currently only being used
with dbcan to ensure users are updated to dbcan3.