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24 lines
847 B
Text
24 lines
847 B
Text
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/*
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* -------------------------------------------------
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* Nextflow config file for GIS (Aquila)
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* -------------------------------------------------
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* Defines reference genomes, using iGenome paths
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* Imported under the default 'standard' Nextflow
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* profile in nextflow.config
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*/
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process {
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executor = 'sge'
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clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/,'') }
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penv = 'OpenMP'
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errorStrategy = { task.attempt < 2 ? 'retry' : 'finish' }
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// auto translate container name into conda environment name
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beforeScript = { 'source /mnt/projects/rpd/rc/init.2017-04; module load miniconda3; set +u; source activate nfcore-rnaseq-1.0dev; set -u;' }
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}
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params {
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saveReference = true
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// illumina iGenomes reference file paths on GIS Aquila
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igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/'
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}
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