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**Command**:
`sudo java -jar cromwell-84.jar run ngs-ubuntu-20-04/iletisim/warp/pipelines/broad/dna_seq/germline/single_sample/exome/local_newGCP_ExomeGermlineSingleSample_deneme6_bcftools.wdl -i ngs…
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**Is your feature request related to a problem? Please describe.**
When the config.yaml has wrong, inconsistent or missing entries the snappy pipeline will fail.
However, in many instances the error…
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Hello,
I'm trying to use the run-ngs-pipeline tool on different genes. The genes without SV works just fine, but I get this error when trying to run it on CYP2D6.
I'm on Ubuntu 24.04.1 LTS.
I …
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Right now whatever is returned from `main()` is used for exit code only.
TODO: Provide a mechanism to indicate that the returned value is to be printed.
Also think how to allow for example `-j` …
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Objective: simulate the science use case that we call “MICADO-SCAO-GaiaRef”. It assesses the achievable accuracy in absolute astrometry for science objects observed with MICADO at the ELT in SCAO mode…
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Hi, I am trying the method to extract phylogenetic markers from NGS data, but an Error occurred from my data or your test dataset, could you share your help? Thank you very much.
Below is the output…
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**Is your feature request related to a problem? Please describe.**
We need to create a minimal cancer variant calling pipeline use case setup here
- https://github.com/bihealth/snappy-use-case-can…
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**Background**
At the moment, Cloud Pipeline allows creating users one-by-one via the GUI. If a number of users shall be created - it would be nice to have a batch creation option.
**Approach**
*…
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Found a minor issue with symlink
if running symlink on a groupby step, Name of datasource is repeated for each job in group.
e.g.
```
/lustre/scratch110/sanger/rg12/Pipeline$ plite symlink -f Mark …