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In GATK4's CNV caller, read depth bins and SNP allele frequencies are segmented separately (by CBS and an HMM, respectively), then intersected (like `GenomicArray.cut`) and a final pass compares adjac…
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Hi
On my previous server, I was able to run Conpair with GATK3.8 but now, on my new server, my java is not compatible with GATK3.8. So I am trying to run Conpair with GATK4.2.3 using the following co…
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### Description of the bug
I am new to nextlfow sarek pipeline, I tried to use docker as profile to test run the sarek pipeline but it had error. is this the docker issue ? how can I download back th…
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We are running joint-discovery-gatk4 in slurm with Cromwell 46.
Only a small fraction of the shards are being processed concurrently.
What adjustments can be made to process more or all shards …
ghost updated
3 years ago
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### Description of feature
i am attempting to install a subworkflow from a custom repository, but i am having issues installing the missing modules from the nf-core/modules repo:
```
$ nf-core subw…
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```diff
$ git checkout develop
$ git --no-pager diff 2020-05-26 -- scripts/Align_mem.sh
diff --git a/scripts/Align_mem.sh b/scripts/Align_mem.sh
index c306a17..7e03c07 100755
--- a/scripts/Align_…
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Using command `stub` blocks in Nextflow is useful when developing syntax and quickly testing pipelines. However, its use within nf-core is limited because the vast majority of nf-core modules do not h…
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I think it would be good to have a module for [gatk4](https://bioconda.github.io/recipes/gatk4/README.html)
Needed for integrating [Gens](https://github.com/Clinical-Genomics-Lund/gens) into the …
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## Bug Report
I run the CNNScoreVariants as tutorial, but it can't continue and always stuck as the following picture, and the programme isn't stop by any error. By the way I can't find gatkcondaenv.…
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gatk_hc.sh script prints `Exception in GATK log ./Logs/GATK4_HC/$sample/$sample.log` to ./Logs/GATK4_HC_error_capture/$sample.err files, even if exception isn't present in .log file.
https://gith…