Stijn van Dongen

Heatmap with pre-defined dendrogram, margin ordering

9

Hello, thank you so much for this fantastic library that I've recently started using. In one of my use cases I have a hiearchical clustering on the columns that is...

The 'failed to populate reference' is an error that can be remedied by taking actions not related to either samtools or input (cram) files. As such, it can be regarded...

support for 10x atac-seq

36

10x atac-seq data does not have UMI. Souporcell gives: ``` Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 104, in assert float(num_umi) / float(num_read_test) > 0.5, "Less than 50% of...

Sorting by name does not guarantee primary alignment sorts before secondary and supplementary

2

Apologies for missing data - this was already confirmed by @jkbonfield . `samtools sort -n` sorts on name. Its secondary sort does not guarantee that within-group (the same read with...

Hello, I'm the mcl upstream maintainer and interested in updating the patches that are in https://github.com/fhcrc/mcl (relative to mcl release 14-137) to the current source tree of mcl (latest released...

KeyError message in assemble

5

Hi, below is the KeyError error that I get with tracer assemble. It is only one out of 1536 samples, so otherwise the software is running very nicely. Below the...

Error handling for processes

59

We would like NF to support metadata tracking and routing; this would for example enable a process to inform another process that an action was not taken or a stage...