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added AVIA_not_found column. It seems AVIA does not have complete MAF list.
Case | Khanlab | AVIA | Both | Khanlab Only | AVIA Only | AVIA Only Not Found | Khanlab Only (%) | AVIA Only (%) | AVIA O…
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biowulf deprecates module versions over time, which breaks our pipelines. switching to containers will make this pipeline more robust.
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Since the primary storage space is not enough, we need to move the data from "biowulf" to S3
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### Notice
There are many files need to be copied from biowulf to S3 in many different folders.
### Detail
Root Path in S3:
lix33/COVID19/UpstreamAnalysis/PostPrimaryRun/Data/10_11_2021/lo…
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The stub run hangs after completion -- nextflow doesn't recognize the processes are all done. This happens on github actions and locally. Doesn't happen on biowulf with lots of memory.
```sh
cd te…
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Just found all of my jobs were killed due to the running time.
For norm partition, the default running time is only 2 hours in Biowulf. You should set it to the maximum running time (10 days) by u…
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Hi,
I installed genome-seek through conda:
```
mamba create -c conda-forge -c bioconda -p /mycondaEnv/snakemake_singularity snakemake singularity
git clone https://github.com/OpenOmics/genome-…
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### Using obj_get
```
file="lix33/COVID19/USU/Data/06_30_2021/ProcessedData/202107_XXXXXX_XXXX_H3NGNDSX2/BAM/BWA/v38/I3-97794_CTTGGTAT-GGACTTGG_L001_HQ_paired_dedup_nophix.bai"
obj_get -v DCEG_CO…