Comments on JOSS article #87
Description
Regarding joss-reviews/issues/9324,
Using Nextflow version 25.04.4 from my institution's HPC, I ran nf-core/coproid using the test data. Here is the script that I ran:
nextflow run nf-core/coproid -r 2.0.0 -profile test,singularity --outdir $OUTDIR -w $WORKDIR -c $CONFIG
I got the following error that seems to be syntax related in coproid/modules/nf-core/sam2lca/analyze/main.nf:
N E X T F L O W ~ version 25.04.4
Launching `https://github.com/nf-core/coproid` [serene_faraday] DSL2 - revision: 56308278ce [2.0.0]
ERROR ~ Module compilation error
- file : /mnt/scratch/vusichjo/nxf_assets/nf-core/coproid/modules/nf-core/sam2lca/analyze/main.nf
- cause: Variable `database` already declared in the process scope @ line 28, column 9.
def database = database ? "${database}" : "sam2lca_db"
^
1 error
-- Check script '/mnt/scratch/vusichjo/nxf_assets/nf-core/coproid/workflows/coproid.nf' at line: 10 or see '.nextflow.log' file for more details