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first working version of maxquant

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veitveit 2021-12-17 12:34:28 +01:00
parent 7e56e38f2a
commit c3f8aca21b
9 changed files with 56617 additions and 114589 deletions
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4
modules/maxquant/lfq/main.nf
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@ -24,7 +24,7 @@ process MAXQUANT_LFQ {
path raw path raw
output: output:
tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt tuple val(meta), path("*.txt"), emit: maxquant_txt
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
@ -37,7 +37,7 @@ process MAXQUANT_LFQ {
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
maxquant mqpar_changed.xml maxquant mqpar_changed.xml
mv combined/txt/*.txt .
""" """
} }

2
tests/config/nextflow.config
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@ -7,7 +7,7 @@ params {
process { process {
cpus = 2 cpus = 2
memory = 3.GB memory = 6.GB
time = 2.h time = 2.h
} }

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tests/modules/maxquant/lfq/OVEMB150205_12.raw
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tests/modules/maxquant/lfq/OVEMB150205_14.raw
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113206
tests/modules/maxquant/lfq/?query=proteome:UP000002311&format=fasta → tests/modules/maxquant/lfq/UP000002311_559292.fasta
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11
tests/modules/maxquant/lfq/main.nf
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@ -5,10 +5,13 @@ nextflow.enable.dsl = 2
include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] ) include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] )
workflow test_maxquant_lfq { workflow test_maxquant_lfq {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true) ] file(params.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true)
rawfiles = file(params.raw) ]
MAXQUANT_LFQ ( input, rawfiles.collect())
rawfiles = [file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_12.raw') , file('https://github.com/wombat-p/MaxQuant-Workflow/raw/dev/Nextflow/data_test/OVEMB150205_14.raw') ]
MAXQUANT_LFQ ( input, rawfiles.collect() )
} }

2
tests/modules/maxquant/lfq/mqpar.xml
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@ -2,7 +2,7 @@
<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<fastaFiles> <fastaFiles>
<FastaFileInfo> <FastaFileInfo>
<fastaFilePath>PLACEHOLDERyeast.fasta</fastaFilePath> <fastaFilePath>PLACEHOLDERyeast_UPS.fasta</fastaFilePath>
<identifierParseRule>&gt;([^\s]*)</identifierParseRule> <identifierParseRule>&gt;([^\s]*)</identifierParseRule>
<descriptionParseRule>&gt;(.*)</descriptionParseRule> <descriptionParseRule>&gt;(.*)</descriptionParseRule>
<taxonomyParseRule></taxonomyParseRule> <taxonomyParseRule></taxonomyParseRule>

5
tests/modules/maxquant/lfq/test.yml
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@ -1,10 +1,11 @@
## 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 mqpar.xml -raw '*.raw' -fasta yeast.fasta -c tests/config/nextflow.config # 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 ./tests/modules/maxquant/lfq/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
- maxquant/lfq - maxquant/lfq
files: files:
- path: output/maxquant/proteinGroups.txt - path: output/maxquant/proteinGroups.txt
md5sum: e667c7caad0bc4b7ac383fd023c654fc md5sum: 2a6461987ace82d3f593ffbd60b65442

57976
tests/modules/maxquant/lfq/yeast.fasta
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