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Well the title says it all,
Big fan of cf, been using it allot on uppmax. Is there a way specify output locations for modules ?
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singleCPUMem = 7.GB in uppmax-slurm.config will allocate two cores to single core jobs on bianca.
7.GB translates to "#SBATCH --mem 7168" in the slurm start scripts and the default MB per core is 700…
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When adding a new genome, one currently needs to edit both `uppmax.config` and `genomes.config`. With `bundleDir` also in `genomes.config`, only one file needs to be customized.
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This is the current diff between `configuration/milou.config` and `configuration/bianca.config`:
```
--- bianca.config 2017-03-20 16:18:49.656447658 +0100
+++ milou.config 2017-03-20 1…
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Hi there
I tried to run CAW on my laptop and followed the instructions on how to run the test data set, but i shuts down with the following error message:
```bash
CAW $ nextflow run main.nf --…
dahlo updated
7 years ago
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**Hello there!**
I followed the scout user examples, I managed to run the following commands:
scout setup database
scout load panel tests/fixtures/gene_lists/panel_1.txt
scout load case tests/fixt…
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I got a problem when running the version of the CAW that was available on January 23 (v0.9.9).
The problem is that somehow the memory parameters in the slurm jobs is set to 131072:
#SBATCH --mem 13…
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Running a regular wgs bam with --steps manta,vep
```nextflow run main.nf --project b2014152 --bam /proj/b2014152/private/delivery/P2109/P2109_150/03-BAM/P2109_150.clean.dedup.recal.bam --steps mant…
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The results only included fastqc and trim_galore. They seemed to be finished. The bwa dir was empty and left tasks were undone.
Here is my config for docker version according my poor understanding…
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> I had a look at your hours and it looks like you are running on about 50% efficiency overall. So half the hours i give you will more or less not be used. It looks like many of the nextflow scripts y…