--input_contigs incompatible with samplesheet validation (expects 3 columns)

[AnnaEwertz]

Description of the bug

I am trying to run the pipeline using pre-assembled contigs via --input_contigs with specification of the path to the contigs file, as described in the documentation. There is also an example samplesheet for contig input is provided with only two columns (viroprofiler/assets/samplesheet_contigs.csv).
However, the pipeline still enforces a 3-column samplesheet (sample,fastq_1,fastq_2) during the INPUT_CHECK step, which makes it impossible to use the contig-only input mode.

Command used and terminal output

### .slurm skript ###

#!/bin/bash
#SBATCH --job-name=viroprofiler
#SBATCH --output=viroprofiler_%j.log
#SBATCH --partition=base
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=20G
#SBATCH --time=24:00:00

export NXF_SINGULARITY_CACHEDIR=/work_beegfs/sbbmi002/ViroProfiler/singularity_cache
export SINGULARITY_CACHEDIR=/work_beegfs/sbbmi002/ViroProfiler/singularity_cache


cd /work_beegfs/sbbmi002/ViroProfiler

nextflow run deng-lab/viroprofiler \
    -r main \
    -profile singularity \
    --conda-prefix /work_beegfs/sbbmi002/ViroProfiler/conda_envs \
    -process.executor slurm \
    --input_contigs /work_beegfs/sbbmi002/ViroProfiler/all_human_samples_contigs.fa \
    --input /work_beegfs/sbbmi002/ViroProfiler/samplesheet_human.csv \
    --max_cpus 8 \
    --max_memory 20.GB \
    --max_time 24.h \
    --use_iphop false \
    --use_dram false \
    -resume
~                    


### output ###

* The ViroProfiler pipeline
 Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
 Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522

* The nf-core framework
 Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
 Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
[-        ] VIROPROFILER:FASTQC            -
[-        ] VIROPROFILER:FASTP             -
[-        ] VIROPROFILER:CHECKV            -
[-        ] VIROPROFILER:CONTIGLIB_CLUSTER -
[-        ] VIROPROFILER:GENEPRED4CTG      -
[-        ] VIROPROFILER:NRPROT            -
[-        ] VIROPROFILER:NRGENE            -
[-        ] VIROPROFILER:CONTIGINDEX       -
[-        ] VIROPROFILER:MAPPING2CONTIGS2  -
[-        ] VIROPROFILER:ABUNDANCE         -

[-        ] VIROPROFILER:FASTQC            -
[-        ] VIROPROFILER:FASTP             -
[-        ] VIROPROFILER:CHECKV            -
[-        ] VIROPROFILER:CONTIGLIB_CLUSTER -
[-        ] VIROPROFILER:GENEPRED4CTG      -
[-        ] VIROPROFILER:NRPROT            -
[-        ] VIROPROFILER:NRGENE            -
[-        ] VIROPROFILER:CONTIGINDEX       -
[-        ] VIROPROFILER:MAPPING2CONTIGS2  -
[-        ] VIROPROFILER:ABUNDANCE         -
[-        ] VIROPROFILER:VIBRANT           -
[-        ] VIROPROFILER:DVF               -
[-        ] VIROPROFILER:VIRCONTIGS_PRE    -
[-        ] VIROPROFILER:VIRSORTER2        -
[-        ] VIROPROFILER:TAXONOMY_VCONTACT -
[-        ] VIROPROFILER:TAXONOMY_MMSEQS   -
[-        ] VIROPROFILER:TAXONOMY_MERGE    -
[-        ] VIROPROFILER:BACPHLIP          -
[-        ] VIROPROFILER:RESULTS_TSE       -
[-        ] VIR…USTOM_DUMPSOFTWAREVERSIONS -
Plus 1 more processes waiting for tasks…
ERROR ~ Input samplesheet contains row with 2 column(s). Expects 3.

 -- Check '.nextflow.log' file for details

(base) [sbbmi002@caucluster1 ViroProfiler]$

Relevant files

samplesheet_human.csv

sample,contigs
contigs,/work_beegfs/sbbmi002/ViroProfiler/all_human_samples_contigs.fa

template in viroprofiler/assets/samplesheet_contigs.csv

System information

N E X T F L O W
version 24.10.5 build 5935
created 04-03-2025 17:55 UTC (18:55 MESZ)
cite doi:10.1038/nbt.3820
http://nextflow.io

HPC

slurm

Singularity

Linux