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## Compile list of Modules to add for Docker Build
module=['vcf2maf/1.6.21','VEP/102']
module=['fastq_screen/0.15.2','bowtie/2-2.5.1']
module=['kraken/2.1.2', 'kronatools/2.8']
mod…
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python /home/kpadmin/biosoft/TMB/bin/pyTMB.py -i /home/kpadmin/TMB/LST_norm.vcf --effGenomeSize 33280000 --dbConfig /home/kpadmin/biosoft/TMB/config/snpeff.yml --varConfig /home/kpadmin/biosoft/TMB/co…
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Hello, Thank you for the great pipeline!
Now, I try to run the pipeline to call SV. I get an error when trying to run sv_pipeline.cwl, the error as below:
```Shell
cwltool /home/liuhui/ctDNA-pipeli…
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I'm running the CTAT-mutations pipeline, and I get the following warning messages that appear during the SNP-eff step. The script stops running at this point, even though I have allocated 50 hours of …
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Thank you for the useful script, but I noticed an error in my output for kaks.py. Because the script totals the numbers of missense and sense SNPs per gene, I found the counts to be redundant for gene…
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Hey,
I was trying to run the tb-profiler on my samples.I am facing this delly issue.Can you please look into it?
# tb-profiler error report
* OS: linux
* Program version: 6.2.1
* Database ver…
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### Description of the bug
After the recent update of the module [bea3ca9](https://github.com/nf-core/modules/commit/bea3ca998816a7f812b1bbbcb27c3a9ffbac0706), `ENSEMBLVEP` process fails:
```
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I am trying this with EasyBuild 2.0.0 and I get an error:
```
[soft@vhircluster easybuild]$ eb --configfiles=easybuild.cfg /tmp/snpEff-4.0-Java-1.7.0_67.eb --try-software-version=4.1 --debug
== tempo…
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I am wondering how can i add something like [Pseudomonas aeruginosa ](https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa#:~:text=Pseudomonas%20aeruginosa%20is%20a%20common,of%20considerable%20medica…
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Hello,
I am trying to use snippy 4.6.0 via miniconda3 on Linux and the output given indicates my samples have 0 variants compared to the reference genome.
The created snps.csv has no data in it and…