Closed joannakraw closed 2 weeks ago
Hi @joannakraw thank you so much!! Would you actually mind opening a PR with your contribution? If you're unsure how to go about it i would be happy to help! Laurence
Hi @LaurenceKuhl, thanks for such a quick reply! I will try to do this, and let you know in case of any problems. Best, Joanna
Hi Joanna,
Thanks!! don't hesitate to just open it and tag me if you have any questions :)
Hi @joannakraw, could you let me know why you re opened this? thanks!
Hi @LaurenceKuhl, I've clicked close by mistake, so I've reopened it again. I didn't know if I'm supposed to close this issue or you, sorry for the confusion!
All good :D I'll close it again, unless you are still experiencing issues even with your bug fix then please re-open it :)
Description of the bug
Problem description:
I encountered an error while running the pipeline with the cutadapt option, specifically when passing adapter sequences using the
five_prime_adapter
andthree_prime_adapter
parameters. The pipeline execution fails with the following error message:Workaround:
I have resolved this issue locally by making the following changes:
CUTADAPT.out
withCUTADAPT_FIVE_PRIME
in line 89.CUTADAPT.out
withCUTADAPT_THREE_PRIME
in line 98. These modifications allowed the pipeline to run without encountering the No such variable error. I attach the whole fragment of the modified code below:Modified code
In the
workflows/crisprseq_screening.nf
:Command used and terminal output
Relevant files
No response
System information
Nextflow info: