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veitveit 2022-01-20 18:02:30 +01:00
parent 2d48ca13ba
commit 98db2b9950
4 changed files with 13 additions and 9 deletions
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8
modules/maxquant/lfq/main.nf
View file

@ -6,7 +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:v0.13" container "wombatp/maxquant-pipeline:v0.13"
} }
input: input:
@ -19,10 +19,10 @@ process MAXQUANT_LFQ {
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:$PATH export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > 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

8
modules/maxquant/lfq/meta.yml
View file

@ -18,18 +18,18 @@ input:
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- raw: - raw:
type: file type: file
description: raw files with mass spectra description: raw files with mass spectra
pattern: "*.{raw,RAW,Raw}" pattern: "*.{raw,RAW,Raw}"
- fasta: - fasta:
type: file type: file
description: fasta file with protein sequences description: fasta file with protein sequences
pattern: "*.{fasta}" pattern: "*.{fasta}"
- parfile: - parfile:
type: file type: file
description: MaxQuant parameter file (XML) description: MaxQuant parameter file (XML)
pattern: "*.{xml}" pattern: "*.{xml}"

5
tests/modules/maxquant/lfq/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

1
tests/modules/maxquant/lfq/test.yml
View file

@ -1,7 +1,6 @@
## TODO nf-core: Please run the following command to build this file: ## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml maxquant/lfq # nf-core modules create-test-yml maxquant/lfq
- name: maxquant lfq - name: maxquant lfq
# command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq --paramfile ./tests/modules/maxquant/lfq/mqpar.xml --raw 'https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_{12,14}.raw' --fasta 'https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/ABRF_iPRG_2012_target.fasta' -c tests/config/nextflow.config
command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq --paramfile 'https://raw.githubusercontent.com/wombat-p/DSL2-data/master/nf-core-modules/test_data/maxquant/mqpar.xml' --fasta 'https://raw.githubusercontent.com/wombat-p/MaxQuant-Workflow/dev/data/yeast_UPS.fasta' -c tests/config/nextflow.config command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq --paramfile 'https://raw.githubusercontent.com/wombat-p/DSL2-data/master/nf-core-modules/test_data/maxquant/mqpar.xml' --fasta 'https://raw.githubusercontent.com/wombat-p/MaxQuant-Workflow/dev/data/yeast_UPS.fasta' -c tests/config/nextflow.config
tags: tags:
- maxquant - maxquant