mirdeep2 output missing

[LucasMcNU]

Description of the bug

Running the smRNAseq pipeline does not produce the output listed here. MirDeep2 output is missing. Everything else is there. Running this on the Northwestern University HPC using their configuration file. Used the following genome file:

projects/genomicsshare/AWS_iGenomes/references/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa

Command I used is below:

Command used and terminal output

## Load modules
module purge

module load nextflow/23.04.3
module load singularity/latest
module load graphviz/2.40.1
module load java/jdk11.0.10

project_dir=/projects/b1042/BackmanLab/Lucas/101823_rnaseq/Backman19_10.18.2023/smallRNA/
cd $project_dir
OUTDIR=${project_dir}nextflow_results/
[ -d $OUTDIR ] || mkdir -p $OUTDIR

nextflow run nf-core/smrnaseq \
-profile nu_genomics \
--input $project_dir/samplesheet.csv \
--genome 'GRCh38' \
--mirtrace_species 'hsa' \
--protocol 'nextflex' \
--outdir $OUTDIR

Relevant files

nextflow.log

System information

No response

[mazzalab]

same here

[apeltzer]

#343 fixed