How to set sample sheet without IgG control?

[cjfields]

Description of the bug

I have tried rerunning the updated cutandrun workflow (v2) using the following sample sheet, based on prior recommendations for skipping IgG controls (set the control to '1' and --igg_control to false):

group,replicate,fastq_1,fastq_2,control
1_1h_1,1,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_1_GCAGAATT-TGGCCGGT_L001_R1_001.fastq.gz,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_1_GCAGAATT-TGGCCGGT_L001_R2_001.fastq.gz,1
1_1h_2,2,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_2_CTCTCGTC-AGGTTATA_L001_R1_001.fastq.gz,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_2_CTCTCGTC-AGGTTATA_L001_R2_001.fastq.gz,1
1_1h_Heat_1,1,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_Heat_1_GCTTGTCA-GTATGTTC_L001_R1_001.fastq.gz,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_Heat_1_GCTTGTCA-GTATGTTC_L001_R2_001.fastq.gz,1
1_1h_Heat_2,2,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_Heat_2_AATCCGGA-AACTGTAG_L001_R1_001.fastq.gz,/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/raw-seq/1_1h_Heat_2_AATCCGGA-AACTGTAG_L001_R2_001.fastq.gz,1

and the following config:

params {
     input = "samplesheet.small.csv"
     save_reference = true
     igg_control = false
     use_control = false
     fasta = "/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/reference/GRCh38_flu_RSV.fa"
     gtf = "/home/groups/hpcbio/references/nextflow/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
     gene_bed = "/home/groups/hpcbio/references/nextflow/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
     blacklist = "/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/reference/ENCFF356LFX.bed"
     dedup_target_reads = false
     email = "[email protected]"
     spikein_fasta = "/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/data/reference/GCF_000146045.2_R64_genomic.fna"
     custom_config_base = "/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/src/configs"
     peakcaller="macs2,seacr"
     replicate_threshold=2
     save_spikein_aligned=true
     skip_upset_plots=false
     skip_reporting=false
}

Anything I'm doing wrong?

Command used and terminal output

Run as follows:


$ nextflow run nf-core/cutandrun -r 2.0 -c cutnrun-yeast.conf -profile uiuc_hpcbio --custom_config_base /home/groups/hpcbio/projects/src/configs -resume -qs 4 -with-report -with-trace

This is the error I'm seeing:

Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.small.csv)'

Caused by:
  Process `NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.small.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py samplesheet.small.csv samplesheet.valid.csv false

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | grep -E -o "([0-9]{1,}\.)+[0-9]{1,}")
  END_VERSIONS

Command exit status:
  1

Command output:
  ERROR: Please check samplesheet -> Each control entry must match at least one group entry! Unmatched control entry: 1.

Command error:

Work dir:
  /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/results/2022-06-14-CUTNRUNv2/work/40/f81d18706ad65dff43bb65d3c12ef9

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

### Relevant files

[nextflow.log](https://github.com/nf-core/cutandrun/files/8905814/nextflow.log)


### System information

CentOS 7 using SIngularity 3.8.1, SLURM on local HPC.  Nextflow 22.04.3

[cjfields]

Closing this, I found out the command line flag changed and the naming convention for replicates has also changed a bit. This now seems to be running!

[chris-cheshire]

hi @cjfields sorry ive been in the lab, just catching up. This is all resolved?

[cjfields]

@chris-cheshire No worries, I figured it out (was a misconfiguration); I guessed you were pretty tied up. This is a more complicated rerun of a larger data set, I'll let you know if I run into issues on Slack.

[wbszhu]

Hi,
I meet the same error. Could you please show me the right way to solve it?
Thanks,
Luzhang

[chris-cheshire]

Please read the documentation here:

https://nf-co.re/cutandrun/2.0/usage

Let me know if you cant work it out.

[yxralba088]

hi,
i meet the same error. Could you please tell me how to solve it?
thanks,
alba

[chris-cheshire]

Does reading the latest docs help?

[yxralba088]

Does reading the latest docs help?

hi, I read the latest docs(version=3.2.2), and I set the control colum to '1' and --use_control to false, but it still can't work. I get the error:

ERROR: Please check samplesheet -> Each control entry must match at least one group entry! Unmatched control entry: 1.

Could you please tell me how I can fix it?

Thanks,
Alba