There is no qiime2 result file in the results

[petemeng]

Description of the bug

There is no qiime2 result file in my results.

Command used and terminal output

nextflow run ampliseq/main.nf \
-profile conda \
--input manifest_new \
--FW_primer ACTCCTACGGGAGGCAGCA \
--RV_primer GGACTACHVGGGTWTCTAAT \
--metadata metadata_new.tsv \
--outdir ./results2 \
--metadata_category condition \
--metadata_category_barplot condition \
--picrust true \
--skip_qiime false

### Relevant files

The resulting file is as follows：
barrnap
cutadapt
dada2
fastqc
input
multiqc
overall_summary.tsv
phyloseq
pipeline_info
summary_report

### System information

Nextflow 23.4.2
ampliseq 2.9.0

[d4straub]

Hi there, the pipeline cannot execute QIIME2 with conda. You should have gotten at least one big warning saying "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." did you not? It is also discouraged to use conda, see https://nf-co.re/ampliseq/2.9.0/docs/usage#-profile Other than that, maybe it would be good to add that warning somewhere in the documentation. Where would you have seen it?

[petemeng]

oh! Thank you very much!!!