Antismash parameter bug

[ewissel]

Description of the bug

As discussed in the slack, the funcscan documentation says that parameter --bgc_antismash_installation is not required when the install is via conda (my set up), and in fact pointing to the conda install with this flag does not work so I removed it. I have predownloaded the antismash database and point to it with --bgc_antismash_databases . However, the pipeline won't run if I don't have both of these parameters, as indicated with the following error message:

[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead).

Command used and terminal output

$ nextflow run nf-core/funcscan -c '/ceph/work/IBMS-PHLab/emily/scripts_general/nextflow_edr1.config' \
    -resume -profile singularity \
    --run_amp_screening --run_arg_screening \
    --run_bgc_screening --save_annotations --save_databases --arg_skip_fargene \
    --arg_skip_rgi --arg_skip_deeparg \
    --input $input_samplesheet \
    --outdir $output_dir \
    --bgc_skip_deepbgc \
    --amp_hmmsearch_models "/ceph/work/IBMS-PHLab/emily/databases/amp_hmm/*.hmm" \
    --bgc_hmmsearch_models "/ceph/work/IBMS-PHLab/emily/databases/deepbgc_db/common/*.hmm" \
    --bgc_antismash_databases "/ceph/work/IBMS-PHLab/emily/databases/antismash/antismash_db/" \    #--arg_amrfinderplus_db '/ceph/work/IBMS-PHLab/emily/nf_ceph/share/amrfinderplus/data/3.12.1/' \\  


[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead).

Relevant files

No response

System information

No response

[jfy133]

Done in #393