Hi
I’ve been trying to use Nextflow to analyze a project.
I’ve setup an AWS environment, and succesfully ran the test version of nf-core rnaseq,
However, when I tried running my own data, I tried inputting my own data on the second screen (Run Parameters). Unfortunately, it seemed to keep some test parameters, when I deleted the original values in this screen.
I ended up copying the rnaseq pipeline, and editing it to delete all predefined parameters including config profile and pipeline parameters. So, starting with the first image (before.jpg) and ending up with the second image (after.jpg).
Is this what I’m supposed to do? If not, how do I overwrite the default pipeline parameters? Changing the run parameters when launching was insufficient.
Regarding the config profile - I’m using AWS Batch via Forge, but there seem to be multiple aws profiles including “awsbatch”, “aws_tower”, “czbiohub_aws”. I’m assuming I should use “awsbatch”, but is there a description somewhere please?
If this is documented, I’d appreciate a link and sorry for spamming.
Yours,
Uri David Akavia