MAGECK mle cnv correction doesn't work

[LaurenceKuhl]

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]

What is the content of user.config?

[LaurenceKuhl]

user.txt

[LaurenceKuhl]

cnv_data.txt

[mirpedrol]

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.