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nf-core / crisprseq

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`).
https://nf-co.re/crisprseq
MIT License
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MAGECK mle cnv correction doesn't work #179

Open LaurenceKuhl opened 1 month ago

LaurenceKuhl commented 1 month ago

Description of the bug

When the user adds a cnv correction with the config file, the pipeline takes ages and then fails count_table.count.txt Brunello_RepA_Dropout_A375_Brunello_RepB_Dropout_A375_vs_Brunello_pDNA.txt

Command used and terminal output

nextflow run crisprseq -r dev -profile cfc --count_table count_table.count.txt --mle_design_matrix Brunello_RepA_Dropout_A375_Brunello_RepB_Dropout_A375_vs_Brunello_pDNA.txt  --outdir test --analysis screening -resume -dump-channels -c user.config

Relevant files

No response

System information

No response

mirpedrol commented 1 month ago

What is the content of user.config?

LaurenceKuhl commented 1 month ago

user.txt

LaurenceKuhl commented 1 month ago

cnv_data.txt

mirpedrol commented 1 month ago

What is happening here is that files have to be staged to the process work directory, so they have to be provided as module inputs. By providing this file through a config it is not staged, so it is not found when running the module.