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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
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Error -input_contigs option "samplesheet not specified" #24

Open ljohanam opened 4 months ago

ljohanam commented 4 months ago

Description of the bug

I really want to run this pipeline, however, I am facing several issues. First, with spades memory, I ran the assemblies out of the pipeline, and I tried to run the pipeline using the input_contigs option, but, although I have made several variants in the params.yml file, the error is always the same: "samplesheet not specified". I do not know if there is something wrong with my settings or if there is an error in the viroprofile configs file.

These are my settings:

============================= Input =======================================

input_contigs: "/media/projects/data/UEB/Viroma_Esp/CGEK34JV230210/pip-2/UB02-scaffolds.fasta" # false or path t> ch_cclib: true #I ran with and without this option

============================= Output ======================================

outdir: "./pip-2/Res"

============================= Optional steps switch ====================================>use_abricate: false

use_decontam: false use_dram: true use_eggnog: false use_iphop: true use_kraken2: false use_phamb: true

============================= Optional steps parameters ================================># kraken2 + bracken

kraken2_db: "viral" kraken2_clean: true save_output_fastqs : false save_reads_assignment : false

Decontamination

decontam_min_similarity: 0.95 contamref_idx: "/project/genomics/jru/data2/db/viroprofiler/contamination_refs/hg19/ref"

Command used and terminal output

No response

Relevant files

No response

System information

No response

sajanraju commented 4 months ago

HI, I´m not from the Viroprofiler team.

But it seems you havent specified the input sheet in your command. Could you fill the last three part in your question?

ljohanam commented 4 months ago

Thank you!

The spreadsheet samples should be not mandatory if the analyses do not start from raw or clean reads.

The command line used it was:

nextflow run deng-lab/viroprofiler -r main -profile singularity -params-file params.yml --max_cpus 40 --max_memory 120.GB

sajanraju commented 4 months ago

I think you still need to mention the sample input file in the command. here is the example from the assets folder.

sample,contigs
contigs,${HOME}/viroprofiler/testdata/viroprofiler-test/contigs.fasta

This is what I understood from the tutorial.