Thomas Krannich

[usability] Is Bcalm path hardcoded?

2

Hi, I am using Reindeer, however, I cannot run the binary outside of the Reindeer install directory as bcalm is not found otherwise. It breaks with: `sh: ./bin/bcalm: No such...

error setting rlimit when --index

1

Hi, I get an error ``` #Monotigs and index constuction... error setting rlimit to 1035 ``` no matter if I run Reindeer with reads or pre-computed unitigs. The calls are...

Fix FORMAT fields for SNP variant records

1

remove unused FORMAT fields from SNP records

VCF header fields missing

3

Hello Fritz & SURVIVOR dev team, ### What. I attempted to use the VCF file generated by SURVIVOR with _bcftools_, as for instance recommended in issue https://github.com/fritzsedlazeck/SURVIVOR/issues/173. However, _bcftools_ suffers...

Cuttlefish as C++ API / header library?

2

I am very interested in using cuttlefish from within C++ code and was wondering if it would be possible for you to provide some kind of C++ API / header...

Install fail - hmmer version out-of-date

1

Hmmer released a new version such that your build script is failing. The `build.sh` at https://github.com/anuradhawick/LRBinner/blob/a5c3a1faba20e908fe888d636942fbccf914448f/build.sh#L14 is not dynamic s.t. it does not track updates. Once I changed everything to...

Dear hap.py developer team, I have a question regarding the output of _som.py_. - **Question:** I ran som.py (v0.3.15) using a short variants callset and a ground truth set. The...

Singularity container execution of pangolin crashes with recent nextflow versions

9

Hi, I noticed that poreCov crashes when running pangolin via singularity and a reasonably modern nextflow version. It seems that recent updates in the path mounting defaults of nextflow broke...

[Question] CI for Variant Calling

5

**Is your feature request related to a problem? Please describe.** No problem here, just a question and an offer. **Describe the solution you'd like** I am currently developing a framework...