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@ -1,6 +1,6 @@
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singularityDir = "$SCRATCH/singularity_images_nextflow"
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singularityModule = "singularity/3.2.1"
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squashfsModule = "squashfs/4.3"
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def singularityDir = set_singularity_path()
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def singularityModule = "singularity/3.2.1"
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def squashfsModule = "squashfs/4.3"
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params {
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config_profile_description = """
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@ -13,11 +13,21 @@ params {
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}
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singularity {
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enabled = true
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cacheDir = singularityDir
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enabled = true
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cacheDir = singularityDir
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}
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process {
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beforeScript = "module load $singularityModule $squashfsModule"
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executor = 'slurm'
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}
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def set_singularity_path() {
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def scratch = System.getenv('SCRATCH')
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if(scratch == null){
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System.err.println("WARNING: prince.config requires the SCRATCH env var to be set.")
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return null
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} else {
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return "$SCRATCH/singularity_images_nextflow"
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}
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}
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