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Code Issues Releases Packages Activity

now with working docker tests

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veitveit 2022-01-21 09:46:17 +01:00
parent ee3be7b8c4
commit 6fafefd007
1 changed files with 2 additions and 2 deletions
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4
modules/maxquant/lfq/main.nf
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@ -24,8 +24,8 @@ 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:$PATH
cat <<-END_VERSIONS > versions.yml
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml