JAFFAL pipeline crashes when singularity is used

[marcDabad]

Description of the bug

JAFFAL pipeline crashes when singularity is used because singularity container has not minimap2 (at least)

Command used and terminal output

nextflow run nf-core/nanoseq--input samplesheet.csv --outdir first --protocol cDNA --skip_demultiplexing --skip_vc --skip_sv -profile slurm,singularity --jaffal_ref_dir ${PWD}/for_jaffal

Relevant files

No response

System information

• Nextflow 22.10.1
• HPC
• slurm
• Singularity
• Centos
• nanoseq 3.1.0