Damon-Lee Pointon

Hi Elaws, Thanks for producing such a robust script, I've been using it quite a bit over the weekend. I've added another 5 fields from the API that I quite...

Dp24 jbrowse only

1

This Re-adds the lib folder that got deleted? Implements the JBrowse only subworkflow, I have confirmed this to work locally.

### Description of feature We should work on making sure that s3 paths work in the future, this maybe difficult as most of the paths provided are actually directories we...

### Description of the bug As described in title ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information _No response_

### Description of feature Add the below line to the relevant modules ``` // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1)...

### Description of feature All tickets at sanger will now only go through RC with exceptions of Bird, Shark and Ad Hoc additions.

BWA-MEM2 is not configurable from modules.config

1

### Description of the bug BWA-mem2 in CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT is hardcoded for the arguments `-5SPCp` rather than accepting args2 which is controlled via modules.config. ### Command used and terminal output _No...