MAGECK mle cnv correction doesn't work
Open
Nobody has claimed this yet.
bug
- Dominant language
- Nextflow
- Stars
- 63
- Forks
- 39
- PR merge metrics
- No merged PRs in 30d
Description
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the supplied nextflow run crisprseq command with count_table.count.txt, the MAGECK design matrix, and user.config. Trace the CNV-correction and MAGECK mle step to identify why execution takes a long time and fails; done means the same command completes successfully with CNV correction enabled.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100