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Commit 035156b7 authored by Venkat Malladi's avatar Venkat Malladi
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Change to new conventions.

parent 998c2bd7
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......@@ -4,59 +4,59 @@ process {
clusterOptions = '--hold'
// Process specific configuration
$checkDesignFile {
withName: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
$trimReads {
withName: trimReads {
module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
cpus = 32
}
$alignReads{
withName: alignReads{
module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/1.6']
cpus = 32
}
$filterReads{
withName: filterReads{
module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'sambamba/0.6.6', 'bedtools/2.26.0']
cpus = 32
}
$experimentQC {
withName: experimentQC {
module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
cpus = 32
}
$convertReads {
withName: convertReads {
module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'bedtools/2.26.0']
cpus = 32
}
$crossReads {
withName: crossReads {
module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2']
cpus = 32
}
$defineExpDesignFiles {
withName: defineExpDesignFiles {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
$poolAndPsuedoReads {
withName: poolAndPsuedoReads {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
$callPeaksMACS {
withName: callPeaksMACS {
module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0']
cpus = 32
}
$consensusPeaks {
withName: consensusPeaks {
module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']
executor = 'local'
}
$peakAnnotation {
withName: peakAnnotation {
module = ['R/3.4.1-gccmkl']
executor = 'local'
}
$diffPeaks {
withName: diffPeaks {
module = ['R/3.4.1-gccmkl']
cpus = 32
}
$motifSearch {
withName: motifSearch {
module = ['python/2.7.x-anaconda', 'meme/4.11.1-gcc-openmpi', 'bedtools/2.26.0']
cpus = 32
}
......
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