Anyone know why a pipeline will only validate the sample sheet and then end successfully without running any other steps? Here is my example:

nextflow run nf-core/nanoseq --input samplesheet.csv --protocol DNA  --skip_demultiplexing --skip_quantification --save_align_intermeds -profile singularity   --call_variants

 N E X T F L O W   ~  version 25.10.4
....

WARN: Access to undefined parameter `enable_conda` -- Initialise it to a default value eg. `params.enable_conda = some_value`
WARN: The `echo` directive has been deprecated - use `debug` instead
executor >  local (1)
[48/f76666] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)              [100%] 1 of 1 ✔
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES                               -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM                    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT                         -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF                       -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES                          -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF                 -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV                      -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG                   -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED                         -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED                      -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                  -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                      -
-[nf-core/nanoseq] Pipeline completed successfully-

My samplesheet:

group,replicate,barcode,input_file,fasta,gtf
dev_FACS_2,1,,/athstore/spec_basecalling/fast5/dev_FACS_2/,/athstore/genome/GRCh38.primary_assembly.genome.fa,/athstore/genome/gencode.v49.primary_assembly.annotation.gtf
DM_untreated_rep3,1,,/athstore/spec_basecalling/fast5/DM_untreated_rep3/,/athstore/genome/GRCh38.primary_assembly.genome.fa,/athstore/genome/gencode.v49.primary_assembly.annotation.gtf

And both input_file directories have many fast5 files. Looking at nanoseq again, it looks like if I want to use the DNA protocol, I have to start with basecalled fastq files... Say it's not so!

I'm pretty sure there is no basecalling in any currently valid or supported version of nanoseq

Darn.. OK.