Error: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

[mdozmorov]

Description of the bug

WARN: Input tuple does not match input set cardinality declared by process `NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN` -- offending value: /path/to/work/eb/4e5e3a3fa9f24739561950cae26c27/genome.edited.fa
ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

This error is reproducible after nextflow clean nf-core/smrnaseq and restarting in the new folder. I'm running the latest nextflow and the pipeline (2.2.3). Skipping this step with --skip_mirdeep helps, but without it the error persists.

Command used and terminal output

nextflow run nf-core/smrnaseq --input ${INPUT} \
  --outdir ${DIROUT} \
  -profile 'singularity' \
  --genome GRCh38 \
  --mirtrace_species 'hsa' \
  --protocol 'illumina'

Relevant files

No response

System information

nextflow version 23.04.3.5875
HPC
local
singularity
CentOS 7
2.2.3

[macrobiotus]

Dear all, thank you for working on this pipeline. I can confirm this from here. Admittedly I keep checking for version 2.2.4 as 2.2.3 doesn't seem to work very well ever since the miRbase links changed.

[apeltzer]

Should be fine with dev now