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Hi @ksahlin !
sorry for bothering you again!
I am trying to run GATK haplotypecaller on reads mapped with Strobealign. The Haplotypecaller ends with an error:
`java.lang.IllegalArgumentException:…
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Hi,
I was wondering how one might go about using bwa-mem2 as a library in the same way you can in the original bwa;
https://github.com/lh3/bwa/blob/master/example.c
or is there now another wa…
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I am attempting to run bwa-mem2 through a singularity container for human 35X whole genome sequence data set with following command. singularity exec /expanse/lustre/projects/scr104/mgujral/singular…
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Hi,
I'm currently evaluating VarDict on a synthetic tumour dataset similar to the ICGC DREAM set. I'm using VarDict version 1.5.2 with the following commands:
Call variants:
```shell
$ VarDi…
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My code and printed output:
> (base) bio-24046:~ jvanderwoude3$ snippy --outdir trial --ref PAO1.gbk --R1 CF1_LeftLower_D12_R1.fastq.gz --R2 CF1_LeftLower_D12_R2.fastq.gz
> [12:13:56] This is snip…
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**Is your feature request related to a problem? Please describe.**
I have a rule using the [bwa mem wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bwa/mem.html) that sometimes …
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When running the process_reseq_1.0.py script, the following error occurs:
`Line : 677 - Error in step A (bwa-mem):
[E::bwa_set_rg] the read group line contained literal characters -- replace with…
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I reported the problem first here: https://www.biostars.org/p/258263/. Reproducing the same here:
-------------------------------------------------------------------------------------------
I have a…
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Hi! im using bwa-mem2 in python using subprocess.run
```
process = subprocess.run(cmd, shell=True)
rc = process.returncode
print("returncode:", rc)
```
e.g. if I deliberately…
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Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test
### Is your feature request related to a problem? Please describe
…