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adjusted maxquant

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This commit is contained in:
veitveit 2022-01-19 15:19:09 +01:00
parent 5e81095694
commit 4770e84bf8
2 changed files with 5 additions and 6 deletions
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9
modules/maxquant/lfq/main.nf
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@ -6,8 +6,7 @@ process MAXQUANT_LFQ {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2" container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
} else { } else {
# container "wombatp/maxquant-pipeline:dev" container "wombatp/maxquant-pipeline:v0.13"
container "quay.io/biocontainers/maxquant:2.0.1.0
} }
input: input:
@ -16,15 +15,15 @@ process MAXQUANT_LFQ {
output: output:
tuple val(meta), path("*.txt"), emit: maxquant_txt tuple val(meta), path("*.txt"), emit: maxquant_txt
path "*.version.txt" , emit: version path "versions.yml" , emit: version
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
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:$PATH
maxquant --version | head -n1 - > maxquant.version.txt echo "maxquant: \$(maxquant --version 2> versions.yml)"
sed \"s_<numThreads>.*_<numThreads>$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

2
modules/maxquant/lfq/meta.yml
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@ -42,7 +42,7 @@ output:
- version: - version:
type: file type: file
description: File containing software version description: File containing software version
pattern: "*.{version.txt}" pattern: "versions.yml"
- maxquant_txt: - maxquant_txt:
type: file type: file
description: tables with peptides and protein information description: tables with peptides and protein information