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Updated iGenomes location

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Rogan Grant 2021-08-03 15:10:54 -05:00
parent 079258ebbb
commit f793ffaace
2 changed files with 2 additions and 3 deletions
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2
conf/nu_genomics.config
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@ -7,7 +7,7 @@ params
max_memory = 190.GB
max_cpus = 40
max_time = 240.h
igenomes_base = "/projects/genomicsshare/igenomes"
igenomes_base = "/projects/genomicsshare/AWS_iGenomes"
}
singularity

3
docs/nu_genomics.md
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@ -32,5 +32,4 @@ module load graphviz/2.40.1
## Use of iGenomes
A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
You can do this by simply using the `--genome <GENOME_ID>` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary.
A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. These files can be found at `/projects/genomicsshare/AWS_iGenomes`. You can do this by simply using the `--genome <GENOME_ID>` parameter. While you can technically "stream" genomes from iGenomes directly using the pipeline, this is a substantial use of bandwidth and resources on both ends, and potentially poses reproducibility issues later on. Please use the local copies unless absolutely necessary, and save your custom genomes to your personal allocation where necessary.