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When attempting to run RENEE on biowulf without containers (debugging #119) I found that the RSEQC tool has been updated on Biowulf, making the version in the config outdated.
Need to update tools.…
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Sample
```
SJ000026/SJRHB026_S ngs_pipeline_SJ000026=SJRHB026_S=20220911
```
Error
```
/data/khanlab2/processed_DATA/ngs_pipeline_SJ000026=SJRHB026_S=20220911_20221220_005858.log
Error in rul…
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Problem occured during migration from `nf-vallidation` to `nf-schema`. Aim is to migrate to newere sample sheet reader function.
Reproducible steps
1. Create new template pipeline
```
# nf-core…
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```
bash /data/CCBR_Pipeliner/Pipelines/CCBR_tobias/v0.3/run_tobias.bash -m=dryrun -w=./ccbr_tobias
Pipeline Dir: /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CCBR_tobias/.v0.3
Git Commit/Tag: d97bc…
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Reported by Alexei:
Similar outputs with `renee --help` and `renee build --help`
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BIOWULF keeps discontinuing certain tools without prior notice. Hence containerize tools to avoid breaking rules of the pipeline.
- [x] CircExplorer
- [ ] CIRI
- [x] CLEAR
- [ ] NCLscan
- [ …
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**Description**
`cleanyerreads` workflow fails in bactopia 3.0.1. This works (with exactly the same data and bactopia flags) in version 3.0.0.
**Steps to Reproduce**
Steps to reproduce the behavi…
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Load all emptyrooms to biowulf
Pick the closest emptyroom to the acq and add to dataset
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I was able to index the standardized vcf files from Delly using tabix -p vcf, but not able to do so for the vcf files from Manta and Lumpy. The error from tabix points to a coordinate in column 5 of …
liud2 updated
4 years ago
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Hi there,
I'm new to using AIRRFlow and Nextflow and I was trying to run some B cell sequencing (10X Genomics, AIRR formatted data) through the AIRRflow pipeline. First, I was able to run the pipel…