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now with working docker tests

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veitveit 2022-01-21 08:54:43 +01:00
parent 77d2d83131
commit ee3be7b8c4
1 changed files with 4 additions and 1 deletions
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5
modules/maxquant/lfq/main.nf
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@ -23,7 +23,10 @@ process MAXQUANT_LFQ {
""" """
export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
mkdir temp mkdir temp