miRDeep2 expects to find the Rfam_index.*.ebwt files in /opt/conda/bin/indexes. This is a problem when running with Singularity because that is not a writable directory. When building this container the most recent version of Rfam fasta files were downloaded, indexed with Bowtie and added to the container in /opt/conda/bin/indexes.
Updates to Rfam will require updates to the container.