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nextflow.config
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nextflow.config
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process {
executor='pbs'
queue='workq'
clusterOptions = '-P berger_common'
errorStrategy = 'retry'
$report {
module = 'Singularity/2.4.2-GCC-5.4.0-2.26'
}
$sortBam {
module = 'SAMtools/1.4-foss-2016b'
}
$generateFastq {
module = 'BEDTools/v2.17.0-goolf-1.4.10'
time = { 5.hour * task.attempt }
}
$kallistoIndex {
module = 'kallisto/0.42.4-linux-x86_64'
}
$quantKallisto {
module = 'kallisto/0.42.4-linux-x86_64'
memory = '62 GB'
}
$STARindex {
module = 'STAR/2.5.2a-foss-2016b'
time = { 5.hour * task.attempt }
memory ='62 GB'
}
$bam2bw {
module = 'deepTools/2.2.4-foss-2015a-Python-2.7.9:SAMtools/1.4-foss-2016b'
memory = '62 GB'
}
$STAR {
module = 'STAR/2.5.2a-foss-2016b'
}
$deseq2 {
module = 'Singularity/2.4.2-GCC-5.4.0-2.26'
}
$kallistoCountMatrix{
module = 'Singularity/2.4.2-GCC-5.4.0-2.26'
}
$starCountMatrix{
module = 'Singularity/2.4.2-GCC-5.4.0-2.26'
}
$STAR_log{
module = 'Singularity/2.4.2-GCC-5.4.0-2.26'
}
}