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Update main.nf

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Harshil Patel 2020-09-16 19:08:24 +01:00 committed by GitHub
parent 436e37bcd0
commit fb44f36f66
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8
software/rsem/calculateexpression/main.nf
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@ -32,6 +32,13 @@ process RSEM_CALCULATEEXPRESSION {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def ioptions = initOptions(options) def ioptions = initOptions(options)
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
strandedness = '--strandedness forward'
} else if (meta.strandedness == 'reverse') {
strandedness = '--strandedness reverse'
}
def paired_end = meta.single_end ? "" : "--paired-end" def paired_end = meta.single_end ? "" : "--paired-end"
""" """
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'` INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
@ -39,6 +46,7 @@ process RSEM_CALCULATEEXPRESSION {
--num-threads $task.cpus \\ --num-threads $task.cpus \\
--temporary-folder ./tmp/ \\ --temporary-folder ./tmp/ \\
$paired_end \\ $paired_end \\
$strandedness \\
$ioptions.args \\ $ioptions.args \\
$reads \\ $reads \\
\$INDEX \\ \$INDEX \\