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new File breaks cloud execution in bcl_demultiplex #5612
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@k1sauce @Aratz @edmundmiller Hey, how are you doing? An idea to solve this issue is to have a parameter called --log_skipped_fastqs so that the user can decide if the file gets created or not.
if false, the file named what do you think? I tested it and opened two pull requests for the demultiplex.nf and the module counterpart: |
@k1sauce how are you doing? would it be possible to ask you ro run a test with the branch I am working on, to check if it fixes the s3 issue? The idea behind it, is that one can set a flag: Testingtrue |
@glichtenstein Thanks working on this. I spent some time thinking more about this too and I think I would like to tackle it a different way, here are my thoughts:
So that being said I also have a branch that I am testing out some changes on that would address this, if you are in agreement I can open a PR after a bit more development and we can review that one instead? |
@glichtenstein I don't want to get ahead of myself but I am thinking of something simple like this
|
@glichtenstein Ok how does this look #5720 If it's ok with you I think this may be the right approach. Then we can add a filter on file size before Falco in the demultiplex workflow. |
@k1sauce, how are you? I've work in this proposal to fix the |
Have you checked the docs?
Description of the bug
This bug relates to the bcl_demultiplex sub workflow.
new File
will not work with cloud storage like s3, see nf-core/tools#354 for reference, need to usefile
instead.Command used and terminal output
No response
Relevant files
No response
System information
No response
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