Hi folks, I am new to using nextflow - so apologies for a simple Q! I am trying to run nf-core/chipseq for TF ChIP in C. elegans, however I am not getting the homer or DESeq2 outputs (though nextflow says it has completed successfully) is there something I am blatantly missing? Any help would be great! Here is the script to run the process, please let me know if there's anything else I can provide:

#!/bin/bash -e

nextflow run nf-core/chipseq -r 2.0.0 -profile "singularity" \
  -c "/mnt/home3/ahringer/mah238/chip_analysis/exp132/nextflow/chip.config" \
  --input "/mnt/home3/ahringer/mah238/chip_analysis/exp132/nextflow/samplesheet.csv" \
  --outdir "/mnt/home3/ahringer/mah238/chip_analysis/exp132/nextflow/results" \
  --fasta "/mnt/home3/ahringer/fnc21/species/elegans/genome/ce11.fa" \
  --gtf "/mnt/home3/ahringer/mah238/10X_analysis/annotations/c_elegans.PRJNA13758.WS285.canonical_geneset.extended_no_ovlp.3prime_extended.rnaseq_corrected.gtf" \
  --aligner "bowtie2" \
  --blacklist "/mnt/home3/ahringer/mah238/10X_analysis/annotations/ce11-blacklist.bed" \
  --keep_dups \
  --macs_gsize 100291840

Hi, it might because you need to have multiple groups and replicates for this processes to execute, see my answer here