Bedtools merge fails #12
Comments
|
Thanks a lot for incorporating PINTS to the nascent transcription processing pipeline! I'll try to reproduce this issue, and report back. |
Closed
liyao001
added a commit
to liyao001/PINTS
that referenced
this issue
Oct 8, 2022
[Changed]: Prints info instead of a warning message when `--min-mu-percent` related issues are detected. [Changed]: Reduce redundancy in the function `peak_calling` by abstracting statements about parsing input files. [Added]: Added a new QC metric on the number of significant calls. If the number of significant calls is too large, PINTS will throw a warning message and suggest users switch to a more strict FDR cutoff.
liyao001
added a commit
that referenced
this issue
Oct 8, 2022
[Fixed]: Fixed GitHub issue [#12](https://github.com/hyulab/PINTS/iss…
|
Sorry for the delay! I reproduced the error with the inputs you provided. This error happened when PINTS tried to merge all predictions while specific type(s) of predictions (bidirectional/divergent/unidirectional peaks) were empty. I fixed this problem in the recent commit, and I'll post updates to nf-core/nascent#39 when the new release is reflected on the bioconda channel. Again, thanks a lot for helping us spot this bug! |
edmundmiller
added a commit
to nf-core/nascent
that referenced
this issue
Oct 31, 2022
edmundmiller
added a commit
to nf-core/nascent
that referenced
this issue
Oct 31, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
With a small test dataset, but it doesn't fail for homer/grohmm
Steps to reproduce
curl -s https://get.nextflow.io | bashNXF_VER=21.10.3 ./nextflow run nf-core/nascent -r pints -profile test,docker --outdir resultsThe text was updated successfully, but these errors were encountered: