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### Operating System
Other Linux (please specify below)
### Other Linux
Rocky Linux v8.6
### Workflow Version
v1.2.1
### CLI command run
```
/scratchc/jblab/nextflow run epi2me-l…
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The snpEff reports were not present in the 'reports' section of platform until I changed the capitalization of `snpEff` to all lower case to match the subdir name
https://github.com/nf-core/sarek/b…
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Hi I am having issue while running snpEff for annotating the vcf file.The process is getting killed while running. What might be causing the issue?
Please see the error mentioned below
```
java…
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There are toolshed identifiers inside Galaxy workflows, but these are not carried forward into the RO-Crate nor to the knowledge graph.
Example, from https://workflowhub.eu/workflows/7 we have `Gen…
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When an error occurs during snpEff database list file download, remove empty file.
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**Describe the bug**
Unable to download mm39
**To Reproduce**
1. SnpEff version: SnpEff version SnpEff 5.2c (build 2024-04-09 12:24)
2. Genome version: mm39
3. SnpEff full command line: `java -…
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### Operating System
Other Linux (please specify below)
### Other Linux
Ubuntu
### Workflow Version
2.0.0
### Workflow Execution
Command line
### EPI2ME Version
_No response_
### CLI command…
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I am running below command for downloading databases as described,
`$ howard databases --assembly=hg19 --download-genomes=~/howard/databases/genomes/current --genomes-folder=~/howard/databases/geno…
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I tried to run snippy with the following genbank file:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/632/635/GCF_008632635.1_ASM863263v1/GCF_008632635.1_ASM863263v1_genomic.gbff.gz
However, the p…
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```
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/395/GCF_003254395.2_Amel_HAv3.1/GCF_003254395.2_Amel_HAv3.1_genomic.fna.gz
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/395/G…