Open ljohanam opened 1 month 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?
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
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.
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
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System information
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