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Merge pull request #222 from ameynert/master
Addition of ATAC-seq pipeline config, updated docs
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commit
efa051b3e4
2 changed files with 26 additions and 2 deletions
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@ -24,4 +24,28 @@ process {
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withName:GatherBQSRReports {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:HaplotypeCaller {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:GenotypeGVCFs {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:Mutect2 {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:MergeMutect2Stats {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:PileupSummariesForMutect2 {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:MergePileupSummaries {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:CalculateContamination {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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withName:FilterMutect2Calls {
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clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
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}
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}
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@ -35,13 +35,13 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul
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## Singularity set-up
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Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
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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 `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
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If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
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```bash
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module load singularity
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export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity/nf-core-rnaseq_v3.0"
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export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity"
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```
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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.
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