A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
Hi there, appreciate these changes as this is my exact use case, but I've found that I'm getting errors when I specify both options in v2.1.1.
I have tried multiple combinations of specifying protospacer and reference in samplesheet and params (running via nextflow tower on aws batch) - the only way that leads to successful pipeline completion is with both specified only in the samplesheet.
When I use only --protospacer I encounter an error on CRISPRSEQ_PLOTTER where the protospacer is passed as [].
When I use --reference as a path to a .fasta I encounter an error on ORIENT_REFERENCE:
Caused by:
No such variable: id -- Check script '.nextflow/assets/nf-core/crisprseq/./workflows/../modules/local/orient_reference.nf' at line: 2
I have tried multiple combinations of specifying
protospacerandreferencein samplesheet and params (running via nextflow tower on aws batch) - the only way that leads to successful pipeline completion is with both specified only in the samplesheet.When I use only
--protospacerI encounter an error onCRISPRSEQ_PLOTTERwhere the protospacer is passed as[].When I use
--referenceas a path to a.fastaI encounter an error onORIENT_REFERENCE:Appreciate any help you may have!
Originally posted by @benemead in https://github.com/nf-core/crisprseq/issues/43#issuecomment-1924515730