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Merge pull request #222 from ameynert/master

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Addition of ATAC-seq pipeline config, updated docs
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ameynert 2021-04-07 09:48:29 +01:00 committed by GitHub
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24
conf/pipeline/sarek/eddie.config
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@ -24,4 +24,28 @@ process {
withName:GatherBQSRReports { withName:GatherBQSRReports {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:HaplotypeCaller {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GenotypeGVCFs {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:Mutect2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:MergeMutect2Stats {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:PileupSummariesForMutect2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:MergePileupSummaries {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:CalculateContamination {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:FilterMutect2Calls {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
} }

4
docs/eddie.md
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@ -35,13 +35,13 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul
## Singularity set-up ## Singularity set-up
Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path below. If some containers for your pipeline run are not present, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again. If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
```bash ```bash
module load singularity module load singularity
export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity/nf-core-rnaseq_v3.0" export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity"
``` ```
Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations. Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.