tdanhorn

Bug fix for sashimi_plot with --plot-label option

2

This should fix it: ```diff --- lib/python2.7/site-packages/misopy/sashimi_plot/Sashimi.py.old 2017-07-20 16:17:22.000000000 -0600 +++ lib/python2.7/site-packages/misopy/sashimi_plot/Sashimi.py 2018-01-30 19:58:18.320473810 -0700 @@ -88,10 +88,10 @@ output_fname = None if plot_label is not None: # Use custom...

## Bug report This is somewhere between a bug report and a feature request. The current behavior can lead to unexpected consequences, tripping up even experienced users. ### Expected behavior...

### Description of the bug The documentation for parameter `--three_prime_clip_r{1,2}` refers to a FastP parameter that doesn't exist, it should be `--trim_tail{1,2}`. ### Command used and terminal output _No response_...

Enable the pipeline to start directly from mapped BAM files

1

### Description of feature This is a more limited version of #1029, which was closed because of concerns that there are too many ways through the pipeline for this to...

The value of `total_ivl_bp` (and anything derived from it) in the output of `bedtools summary` is incorrect if the intervals in the input BED/GTF/VCF overlap. The reason is that this...

Valid `--mirtrace_species` is required even with `--mirgenedb` when `--mirgenedb_species` is given

4

### Description of the bug According to the documentation, it appears that the miRNA databases miRBase (used by default) and MirGeneDB are alternative sources of reference files, and either can...

Intervals BED file processing: remove headers and validate any timing information

2

### Description of feature The BED file (or, alternatively, `*.intervals_list` file as used by Picard Tools) file that is being passed to sarek (since version 3.0) with the `--intervals` parameter...

Fix samplesheet validation

7

## PR checklist - [ x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...