Ryan James Kennedy

Add gatk cnvcaller

2

## PR checklist Adds gatk's germline cnv caller modules (PreprocessIntervals, CollectReadCounts, AnnotateIntervals, FilterIntervals) and the respective test files - [x] This comment contains a description of changes (with reason). -...

ResFinder version needs to be updated

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Resfinder is currently sitting on v4.1.11 instead of v4.4.2 which is incompatible with the latest database.

Create recipe for ShigaPass v1.5.0

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According to their [publication](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000961), [ShigaPass](https://github.com/imanyass/ShigaPass) is the best performing differentiator when it comes to EIEC and Shigella spp. via serotype prediction. Thus I was wondering if I could add its...

Update tbdb with user-specified reference genome doesn’t work

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I tried running the following given the GCF file provided by NCBI and it didn’t work: ``` singularity exec --bind /data depot.galaxyproject.org-singularity-tb-profiler-6.2.0--pyhdfd78af_1.img tb-profiler update_tbdb --match_ref /path/to/genomes/GCF_000195955.2.fasta --prefix converged_who_fohm_tbdb -d /path/to/tbdb/...

TBProfiler load_library cannot find newly created tbdb

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Upon running the following command: ``` tb-profiler load_library test ``` The following error was returned: ``` Traceback (most recent call last): File "/data/bnf/sw/miniconda3/envs/tbprofiler/bin/tb-profiler", line 565, in args.func(args) File "/data/bnf/sw/miniconda3/envs/tbprofiler/bin/tb-profiler", line...

Version argument CLI

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SMNCopyNumberCaller is in our nextflow pipeline where we have a stub to collect the versions of each software include in the pipeline. It would be nice if `smn_caller.py` had a...