bunch of hacks for control flow#4
Open
JWDebler wants to merge 2 commits intorobsyme:masterfrom
Open
Conversation
The problem was that if one of the two processes (recentLTRs or olderLTRs) does not find any hits, that leads to a bunch of empty files being created. Those empty files then trip up other processes downstream and crash the whole pipeline. This should probably be solved using native nextflow control structures, but I worked around that by creating empty or dummy files wherever necessary. Now at least the pipeline runs through, but I am not sure if or how these dummy files influence other programs in the pipeline.
I used the wrong comment characters in my earlier patch. These added dummy files are still necessary in the latest iteration of nf-repeatmasking since the pipeline does crash otherwise.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The problem was that if one of the two processes (recentLTRs or olderLTRs) does not find any hits, that leads to a bunch of empty files being created. Those empty files then trip up other processes downstream and crash the whole pipeline. This should probably be solved using native nextflow control structures, but I worked around that by creating empty or dummy files wherever necessary.
Now at least the pipeline runs through, but I am not sure if or how these dummy files influence other programs in the pipeline.