ERROR ~ toIndex = 2 -- Check script 'genomenote/./workflows/genomenote.nf' at line: 98

[mdozmorov]

Description of the bug

Hi. I'm interested in trying this pipeline, but running into issues. The main one is the error immediately after running:

ERROR ~ toIndex = 2

 -- Check script 'genomenote/./workflows/genomenote.nf' at line: 98 or see '.nextflow.log' file for more details

My commands and the sample sheet are below. Thanks!

Command used and terminal output

DIRIN=/mount/home/user/data/WorkData/proj1/2023-08.HiC_test
INPUT=${DIRIN}/samplesheet_genomenote.csv
DIROUT=${DIRIN}/OUT_genomenote
GENOME=/mount/home/user/data/ExtData/UCSC/hg38/hg38.fa
nextflow run sanger-tol/genomenote --input ${INPUT} \
  --outdir ${DIROUT} \
  --fasta ${GENOME} \
  -profile singularity

Relevant files

sample,datatype,datafile sample1,hic,/mount/home/user/data/WorkData/proj1/2023-08.HiC_test/sample1/data/aligned/merged_dedup.bam sample2,hic,/mount/home/user/data/WorkData/proj1/2023-08.HiC_test/sample2/data/aligned/merged_dedup.bam

System information

Nextflow version 23.04.3 build 5875 HPC local singularity CentOS latest cloned sanger-tol/genomenote