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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Missing options c1 and c2 with kallistobustools count #123

Closed Khajidu closed 2 years ago

Khajidu commented 2 years ago

Description of the bug

Whenever I launch scrnaseq with --aligner kallisto, it crashes at the counting step with the following error message: kb count: error: the following arguments are required: -c1, -c2. Is something missing from the previous steps?

Command used and terminal output

nextflow run nf-core/scrnaseq -resume --max_memory '500.GB' -r dev -c /shared/home/hmayeur/.nextflow/config --outdir /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/fulltest/ --protocol '10XV3' --aligner kallisto --transcript_fasta /shared/projects/bsbii/sc_single_cell_brain/sc_gene_models_ncbi_utrs.fasta --input 'test_samples_v2.csv' --genome_fasta /shared/projects/bsbii/sc_single_cell_brain/sc_ncbi_genome.fasta --gtf /shared/projects/bsbii/sc_single_cell_brain/sc_gene_models_ncbi_no_genes_no_contigs_notrnas.gtf --kb_workflow 'nucleus' -profile ifb_core

Relevant files

No response

System information

Nextflow version : 22.04.0 Hardware : HPC Executor : Slurm Container : Singularity OS : CentOS Version of nf-core/scrnaseq : 2.0.0 or dev

apeltzer commented 2 years ago

PR is open for a fix for this, not long and it should work perfectly fine then.

apeltzer commented 2 years ago

Should be fine with dev now - please give this a spin and reopen if the problem persists 👍🏻 @Khajidu