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first maxquant
This commit is contained in:
veitveit
parent
d255e00f7a
commit
7e56e38f2a
11 changed files with 116448 additions and 38 deletions
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@ -1,11 +1,6 @@
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// Import generic module functions
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
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// All other parameters MUST be provided as a string i.e. "options.args"
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// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
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// Any parameters that need to be evaluated in the context of a particular sample
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// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
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params.options = [:]
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params.options = [:]
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options = initOptions(params.options)
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options = initOptions(params.options)
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@ -19,45 +14,30 @@ process MAXQUANT_LFQ {
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conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
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conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
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container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
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} else {
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} else {
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container "quay.io/biocontainers/quay.io/biocontainers/maxquant:2.0.1.0--py39hdfd78af_2"
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container "wombatp/maxquant-pipeline:dev"
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}
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}
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input:
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input:
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// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
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tuple val(meta), path(fasta), path(paramfile)
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// MUST be provided as an input via a Groovy Map called "meta".
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path raw
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// This information may not be required in some instances e.g. indexing reference genome files:
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// https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
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// TODO nf-core: Where applicable please provide/convert compressed files as input/output
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// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
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tuple val(meta), path(raw), path(paramfile)
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output:
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output:
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// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
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tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt
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tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt
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// TODO nf-core: List additional required output channels/values here
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path "*.version.txt" , emit: version
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path "*.version.txt" , emit: version
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script:
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script:
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def software = getSoftwareName(task.process)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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// TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
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// If the software is unable to output a version number on the command-line then it can be manually specified
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// e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
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// TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
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// TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
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// using the Nextflow "task" variable e.g. "--threads $task.cpus"
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// TODO nf-core: Please replace the example samtools command below with your module's command
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// TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
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"""
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"""
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maxquant --version > maxquant.version.txt
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# Write number of threads into parameter file
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maxquant --version | head -n1 - > maxquant.version.txt
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sed "s_\<numThreads\>.*_\<numThreads\>12\<\/numThreads\>_" ${paramfile}
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sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
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# Correct folder names
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sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
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sed -i "s|PLACEHOLDER|\$PWD/|g" "${paramfile}"
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mkdir temp
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mkdir temp
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maxquant ${paramfile}
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maxquant mqpar_changed.xml
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"""
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"""
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}
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}
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@ -1,11 +1,9 @@
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name: maxquant_lfq
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name: maxquant_lfq
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## TODO nf-core: Add a description of the module and list keywords
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description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
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description: write your description here
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keywords:
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keywords:
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- sort
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- sort
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tools:
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tools:
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- maxquant:
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- maxquant:
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## TODO nf-core: Add a description and other details for the software below
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description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
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description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
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homepage: None
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homepage: None
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documentation: None
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documentation: None
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@ -13,20 +11,28 @@ tools:
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doi: ""
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doi: ""
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licence: ['http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf']
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licence: ['http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf']
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## TODO nf-core: Add a description of all of the variables used as input
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input:
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input:
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- meta:
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- meta:
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type: map
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type: map
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description: |
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description: |
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Groovy Map containing sample information
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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e.g. [ id:'test', single_end:false ]
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## TODO nf-core: Delete / customise this example input
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- raw:
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type: file
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description: raw files with mass spectra
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pattern: "*.{raw,RAW,Raw}"
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- fasta:
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type: file
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description: fasta file with protein sequences
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pattern: "*.{fasta}"
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- parfile:
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- parfile:
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type: file
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type: file
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description: MaxQuant parameter file (XML)
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description: MaxQuant parameter file (XML)
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pattern: "*.{xml}"
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pattern: "*.{xml}"
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## TODO nf-core: Add a description of all of the variables used as output
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output:
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output:
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- meta:
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- meta:
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type: map
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type: map
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@ -37,7 +43,6 @@ output:
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type: file
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type: file
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description: File containing software version
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description: File containing software version
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pattern: "*.{version.txt}"
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pattern: "*.{version.txt}"
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## TODO nf-core: Delete / customise this example output
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- maxquant_txt:
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- maxquant_txt:
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type: file
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type: file
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description: tables with peptides and protein information
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description: tables with peptides and protein information
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2
modules/maxquant/lfq/t
Normal file
2
modules/maxquant/lfq/t
Normal file
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@ -0,0 +1,2 @@
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[?1h=[6n[H[2JMaxQuantCmd 1.6.10.43
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[?1l>[39;49m
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@ -454,6 +454,14 @@ mash/sketch:
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- modules/mash/sketch/**
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- modules/mash/sketch/**
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- tests/modules/mash/sketch/**
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- tests/modules/mash/sketch/**
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maxquant/lfq:
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- modules/maxquant/lfq/**
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- tests/modules/maxquant/lfq/**
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maxquant/protemics:
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- modules/maxquant/protemics/**
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- tests/modules/maxquant/protemics/**
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metaphlan3:
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metaphlan3:
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- modules/metaphlan3/**
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- modules/metaphlan3/**
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- tests/modules/metaphlan3/**
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- tests/modules/metaphlan3/**
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57976
tests/modules/maxquant/lfq/?query=proteome:UP000002311&format=fasta
Normal file
57976
tests/modules/maxquant/lfq/?query=proteome:UP000002311&format=fasta
Normal file
File diff suppressed because it is too large
Load diff
BIN
tests/modules/maxquant/lfq/OVEMB150205_12.raw
Normal file
BIN
tests/modules/maxquant/lfq/OVEMB150205_12.raw
Normal file
Binary file not shown.
BIN
tests/modules/maxquant/lfq/OVEMB150205_14.raw
Normal file
BIN
tests/modules/maxquant/lfq/OVEMB150205_14.raw
Normal file
Binary file not shown.
14
tests/modules/maxquant/lfq/main.nf
Normal file
14
tests/modules/maxquant/lfq/main.nf
Normal file
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@ -0,0 +1,14 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] )
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workflow test_maxquant_lfq {
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input = [ [ id:'test' ], // meta map
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file(params.fasta, checkIfExists: true), file(params.paramfile, checkIfExists: true) ]
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rawfiles = file(params.raw)
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MAXQUANT_LFQ ( input, rawfiles.collect())
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}
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439
tests/modules/maxquant/lfq/mqpar.xml
Normal file
439
tests/modules/maxquant/lfq/mqpar.xml
Normal file
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@ -0,0 +1,439 @@
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<?xml version="1.0" encoding="utf-8"?>
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<MaxQuantParams xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<fastaFiles>
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<FastaFileInfo>
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<fastaFilePath>PLACEHOLDERyeast.fasta</fastaFilePath>
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<identifierParseRule>>([^\s]*)</identifierParseRule>
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<descriptionParseRule>>(.*)</descriptionParseRule>
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<taxonomyParseRule></taxonomyParseRule>
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<variationParseRule></variationParseRule>
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<modificationParseRule></modificationParseRule>
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<taxonomyId></taxonomyId>
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</FastaFileInfo>
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</fastaFiles>
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<fastaFilesProteogenomics></fastaFilesProteogenomics>
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<fastaFilesFirstSearch></fastaFilesFirstSearch>
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<fixedSearchFolder></fixedSearchFolder>
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<andromedaCacheSize>350000</andromedaCacheSize>
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<advancedRatios>True</advancedRatios>
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<pvalThres>0.005</pvalThres>
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<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
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<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
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<rtShift>False</rtShift>
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<separateLfq>False</separateLfq>
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<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
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<lfqRequireMsms>True</lfqRequireMsms>
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<decoyMode>revert</decoyMode>
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<boxCarMode>all</boxCarMode>
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<includeContaminants>True</includeContaminants>
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<maxPeptideMass>4600</maxPeptideMass>
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<epsilonMutationScore>True</epsilonMutationScore>
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<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
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<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
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<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
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<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
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<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
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<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
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<secondPeptide>True</secondPeptide>
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<matchBetweenRuns>True</matchBetweenRuns>
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<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
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<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
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<dependentPeptides>False</dependentPeptides>
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<dependentPeptideFdr>0</dependentPeptideFdr>
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<dependentPeptideMassBin>0</dependentPeptideMassBin>
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<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
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<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
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<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
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<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
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<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
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<msmsConnection>False</msmsConnection>
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<ibaq>False</ibaq>
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<top3>False</top3>
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<independentEnzymes>False</independentEnzymes>
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<useDeltaScore>False</useDeltaScore>
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<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
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<taxonomyLevel>Species</taxonomyLevel>
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<avalon>False</avalon>
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<nModColumns>3</nModColumns>
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<ibaqLogFit>False</ibaqLogFit>
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<razorProteinFdr>True</razorProteinFdr>
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<deNovoSequencing>False</deNovoSequencing>
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<deNovoVarMods>True</deNovoVarMods>
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<massDifferenceSearch>False</massDifferenceSearch>
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<isotopeCalc>False</isotopeCalc>
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<writePeptidesForSpectrumFile></writePeptidesForSpectrumFile>
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<intensityPredictionsFile></intensityPredictionsFile>
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<minPepLen>7</minPepLen>
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<psmFdrCrosslink>0.01</psmFdrCrosslink>
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<peptideFdr>0.01</peptideFdr>
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<proteinFdr>0.01</proteinFdr>
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<siteFdr>0.01</siteFdr>
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<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
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<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
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<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
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<minPeptides>1</minPeptides>
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<minRazorPeptides>1</minRazorPeptides>
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<minUniquePeptides>0</minUniquePeptides>
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<useCounterparts>False</useCounterparts>
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<advancedSiteIntensities>True</advancedSiteIntensities>
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<customProteinQuantification>False</customProteinQuantification>
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<customProteinQuantificationFile></customProteinQuantificationFile>
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<minRatioCount>2</minRatioCount>
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<restrictProteinQuantification>True</restrictProteinQuantification>
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<restrictMods>
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<string>Oxidation (M)</string>
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<string>Acetyl (Protein N-term)</string>
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</restrictMods>
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<matchingTimeWindow>0.7</matchingTimeWindow>
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<matchingIonMobilityWindow>0.05</matchingIonMobilityWindow>
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<alignmentTimeWindow>20</alignmentTimeWindow>
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<alignmentIonMobilityWindow>1</alignmentIonMobilityWindow>
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<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
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<compositionPrediction>0</compositionPrediction>
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<quantMode>1</quantMode>
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<massDifferenceMods></massDifferenceMods>
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<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
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<writeMsScansTable>True</writeMsScansTable>
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<writeMsmsScansTable>True</writeMsmsScansTable>
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<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
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<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
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<writeMs3ScansTable>True</writeMs3ScansTable>
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<writeAllPeptidesTable>True</writeAllPeptidesTable>
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<writeMzRangeTable>True</writeMzRangeTable>
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<writeMzTab>True</writeMzTab>
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<disableMd5>False</disableMd5>
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<cacheBinInds>True</cacheBinInds>
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<etdIncludeB>False</etdIncludeB>
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<ms2PrecursorShift>0</ms2PrecursorShift>
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<complementaryIonPpm>20</complementaryIonPpm>
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<variationParseRule></variationParseRule>
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<variationMode>none</variationMode>
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<useSeriesReporters>False</useSeriesReporters>
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<name>Session1</name>
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<maxQuantVersion>1.6.10.43</maxQuantVersion>
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<tempFolder>PLACEHOLDERtemp</tempFolder>
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<pluginFolder></pluginFolder>
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<numThreads>2</numThreads>
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<emailAddress></emailAddress>
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<smtpHost></smtpHost>
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<emailFromAddress></emailFromAddress>
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<fixedCombinedFolder></fixedCombinedFolder>
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<fullMinMz>-1.79769313486232E+308</fullMinMz>
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<fullMaxMz>1.79769313486232E+308</fullMaxMz>
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<sendEmail>False</sendEmail>
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<ionCountIntensities>False</ionCountIntensities>
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<verboseColumnHeaders>False</verboseColumnHeaders>
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<calcPeakProperties>False</calcPeakProperties>
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<showCentroidMassDifferences>False</showCentroidMassDifferences>
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<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
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<useDotNetCore>False</useDotNetCore>
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<filePaths>
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<string>PLACEHOLDEROVEMB150205_12.raw</string>
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<string>PLACEHOLDEROVEMB150205_14.raw</string>
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</filePaths>
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<experiments>
|
||||||
|
<string>Sample 1_Tr_1</string>
|
||||||
|
<string>Sample 1_Tr_2</string>
|
||||||
|
</experiments>
|
||||||
|
<fractions>
|
||||||
|
<short>1</short>
|
||||||
|
<short>1</short>
|
||||||
|
</fractions>
|
||||||
|
<ptms>
|
||||||
|
<boolean>False</boolean>
|
||||||
|
<boolean>False</boolean>
|
||||||
|
</ptms>
|
||||||
|
<paramGroupIndices>
|
||||||
|
<int>0</int>
|
||||||
|
<int>0</int>
|
||||||
|
</paramGroupIndices>
|
||||||
|
<referenceChannel>
|
||||||
|
<string></string>
|
||||||
|
<string></string>
|
||||||
|
</referenceChannel>
|
||||||
|
<intensPred>False</intensPred>
|
||||||
|
<intensPredModelReTrain>False</intensPredModelReTrain>
|
||||||
|
<parameterGroups>
|
||||||
|
<parameterGroup>
|
||||||
|
<msInstrument>0</msInstrument>
|
||||||
|
<maxCharge>7</maxCharge>
|
||||||
|
<minPeakLen>2</minPeakLen>
|
||||||
|
<diaMinPeakLen>2</diaMinPeakLen>
|
||||||
|
<useMs1Centroids>False</useMs1Centroids>
|
||||||
|
<useMs2Centroids>False</useMs2Centroids>
|
||||||
|
<cutPeaks>True</cutPeaks>
|
||||||
|
<gapScans>1</gapScans>
|
||||||
|
<minTime>NaN</minTime>
|
||||||
|
<maxTime>NaN</maxTime>
|
||||||
|
<matchType>MatchFromAndTo</matchType>
|
||||||
|
<intensityDetermination>0</intensityDetermination>
|
||||||
|
<centroidMatchTol>8</centroidMatchTol>
|
||||||
|
<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
|
||||||
|
<centroidHalfWidth>35</centroidHalfWidth>
|
||||||
|
<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
|
||||||
|
<valleyFactor>1.4</valleyFactor>
|
||||||
|
<isotopeValleyFactor>1.2</isotopeValleyFactor>
|
||||||
|
<advancedPeakSplitting>False</advancedPeakSplitting>
|
||||||
|
<intensityThreshold>0</intensityThreshold>
|
||||||
|
<labelMods>
|
||||||
|
<string></string>
|
||||||
|
</labelMods>
|
||||||
|
<lcmsRunType>Standard</lcmsRunType>
|
||||||
|
<reQuantify>False</reQuantify>
|
||||||
|
<lfqMode>1</lfqMode>
|
||||||
|
<lfqSkipNorm>False</lfqSkipNorm>
|
||||||
|
<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
|
||||||
|
<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
|
||||||
|
<lfqMaxFeatures>100000</lfqMaxFeatures>
|
||||||
|
<neucodeMaxPpm>0</neucodeMaxPpm>
|
||||||
|
<neucodeResolution>0</neucodeResolution>
|
||||||
|
<neucodeResolutionInMda>False</neucodeResolutionInMda>
|
||||||
|
<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
|
||||||
|
<fastLfq>True</fastLfq>
|
||||||
|
<lfqRestrictFeatures>False</lfqRestrictFeatures>
|
||||||
|
<lfqMinRatioCount>2</lfqMinRatioCount>
|
||||||
|
<maxLabeledAa>0</maxLabeledAa>
|
||||||
|
<maxNmods>5</maxNmods>
|
||||||
|
<maxMissedCleavages>2</maxMissedCleavages>
|
||||||
|
<multiplicity>1</multiplicity>
|
||||||
|
<enzymeMode>0</enzymeMode>
|
||||||
|
<complementaryReporterType>0</complementaryReporterType>
|
||||||
|
<reporterNormalization>0</reporterNormalization>
|
||||||
|
<neucodeIntensityMode>0</neucodeIntensityMode>
|
||||||
|
<fixedModifications>
|
||||||
|
<string>Carbamidomethyl (C)</string>
|
||||||
|
</fixedModifications>
|
||||||
|
<enzymes>
|
||||||
|
<string>Trypsin/P</string>
|
||||||
|
</enzymes>
|
||||||
|
<enzymesFirstSearch></enzymesFirstSearch>
|
||||||
|
<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
|
||||||
|
<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
|
||||||
|
<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
|
||||||
|
<variableModifications>
|
||||||
|
<string>Oxidation (M)</string>
|
||||||
|
<string>Acetyl (Protein N-term)</string>
|
||||||
|
</variableModifications>
|
||||||
|
<useMultiModification>False</useMultiModification>
|
||||||
|
<multiModifications></multiModifications>
|
||||||
|
<isobaricLabels></isobaricLabels>
|
||||||
|
<neucodeLabels></neucodeLabels>
|
||||||
|
<variableModificationsFirstSearch></variableModificationsFirstSearch>
|
||||||
|
<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
|
||||||
|
<additionalVariableModifications></additionalVariableModifications>
|
||||||
|
<additionalVariableModificationProteins></additionalVariableModificationProteins>
|
||||||
|
<doMassFiltering>True</doMassFiltering>
|
||||||
|
<firstSearchTol>0.01</firstSearchTol>
|
||||||
|
<mainSearchTol>0.8</mainSearchTol>
|
||||||
|
<searchTolInPpm>True</searchTolInPpm>
|
||||||
|
<isotopeMatchTol>2</isotopeMatchTol>
|
||||||
|
<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
|
||||||
|
<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
|
||||||
|
<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
|
||||||
|
<checkMassDeficit>True</checkMassDeficit>
|
||||||
|
<recalibrationInPpm>True</recalibrationInPpm>
|
||||||
|
<intensityDependentCalibration>False</intensityDependentCalibration>
|
||||||
|
<minScoreForCalibration>70</minScoreForCalibration>
|
||||||
|
<matchLibraryFile>False</matchLibraryFile>
|
||||||
|
<libraryFile></libraryFile>
|
||||||
|
<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
|
||||||
|
<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
|
||||||
|
<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
|
||||||
|
<reporterMassTolerance>NaN</reporterMassTolerance>
|
||||||
|
<reporterPif>NaN</reporterPif>
|
||||||
|
<filterPif>False</filterPif>
|
||||||
|
<reporterFraction>NaN</reporterFraction>
|
||||||
|
<reporterBasePeakRatio>NaN</reporterBasePeakRatio>
|
||||||
|
<timsHalfWidth>0</timsHalfWidth>
|
||||||
|
<timsStep>0</timsStep>
|
||||||
|
<timsResolution>0</timsResolution>
|
||||||
|
<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
|
||||||
|
<timsRemovePrecursor>True</timsRemovePrecursor>
|
||||||
|
<timsIsobaricLabels>False</timsIsobaricLabels>
|
||||||
|
<timsCollapseMsms>True</timsCollapseMsms>
|
||||||
|
<crosslinkSearch>False</crosslinkSearch>
|
||||||
|
<crossLinker></crossLinker>
|
||||||
|
<minMatchXl>0</minMatchXl>
|
||||||
|
<minPairedPepLenXl>6</minPairedPepLenXl>
|
||||||
|
<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
|
||||||
|
<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
|
||||||
|
<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
|
||||||
|
<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
|
||||||
|
<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
|
||||||
|
<crosslinkModifications></crosslinkModifications>
|
||||||
|
<crosslinkFastaFiles></crosslinkFastaFiles>
|
||||||
|
<crosslinkSites></crosslinkSites>
|
||||||
|
<crosslinkNetworkFiles></crosslinkNetworkFiles>
|
||||||
|
<crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
|
||||||
|
<peakRefinement>False</peakRefinement>
|
||||||
|
<isobaricSumOverWindow>True</isobaricSumOverWindow>
|
||||||
|
<tisobaricWeightExponent>0.75</tisobaricWeightExponent>
|
||||||
|
<diaLibraryType>0</diaLibraryType>
|
||||||
|
<diaLibraryPath></diaLibraryPath>
|
||||||
|
<diaPeptidePaths></diaPeptidePaths>
|
||||||
|
<diaEvidencePaths></diaEvidencePaths>
|
||||||
|
<diaMsmsPaths></diaMsmsPaths>
|
||||||
|
<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
|
||||||
|
<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
|
||||||
|
<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
|
||||||
|
<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
|
||||||
|
<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
|
||||||
|
<diaScoreN>7</diaScoreN>
|
||||||
|
<diaMinScore>2.99</diaMinScore>
|
||||||
|
<diaPrecursorQuant>False</diaPrecursorQuant>
|
||||||
|
<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
|
||||||
|
</parameterGroup>
|
||||||
|
</parameterGroups>
|
||||||
|
<msmsParamsArray>
|
||||||
|
<msmsParams>
|
||||||
|
<Name>FTMS</Name>
|
||||||
|
<MatchTolerance>20</MatchTolerance>
|
||||||
|
<MatchToleranceInPpm>True</MatchToleranceInPpm>
|
||||||
|
<DeisotopeTolerance>7</DeisotopeTolerance>
|
||||||
|
<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
|
||||||
|
<DeNovoTolerance>10</DeNovoTolerance>
|
||||||
|
<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
|
||||||
|
<Deisotope>True</Deisotope>
|
||||||
|
<Topx>12</Topx>
|
||||||
|
<TopxInterval>100</TopxInterval>
|
||||||
|
<HigherCharges>True</HigherCharges>
|
||||||
|
<IncludeWater>True</IncludeWater>
|
||||||
|
<IncludeAmmonia>True</IncludeAmmonia>
|
||||||
|
<DependentLosses>True</DependentLosses>
|
||||||
|
<Recalibration>False</Recalibration>
|
||||||
|
</msmsParams>
|
||||||
|
<msmsParams>
|
||||||
|
<Name>ITMS</Name>
|
||||||
|
<MatchTolerance>0.5</MatchTolerance>
|
||||||
|
<MatchToleranceInPpm>False</MatchToleranceInPpm>
|
||||||
|
<DeisotopeTolerance>0.15</DeisotopeTolerance>
|
||||||
|
<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
|
||||||
|
<DeNovoTolerance>0.25</DeNovoTolerance>
|
||||||
|
<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
|
||||||
|
<Deisotope>False</Deisotope>
|
||||||
|
<Topx>8</Topx>
|
||||||
|
<TopxInterval>100</TopxInterval>
|
||||||
|
<HigherCharges>True</HigherCharges>
|
||||||
|
<IncludeWater>True</IncludeWater>
|
||||||
|
<IncludeAmmonia>True</IncludeAmmonia>
|
||||||
|
<DependentLosses>True</DependentLosses>
|
||||||
|
<Recalibration>False</Recalibration>
|
||||||
|
</msmsParams>
|
||||||
|
<msmsParams>
|
||||||
|
<Name>TOF</Name>
|
||||||
|
<MatchTolerance>40</MatchTolerance>
|
||||||
|
<MatchToleranceInPpm>True</MatchToleranceInPpm>
|
||||||
|
<DeisotopeTolerance>0.01</DeisotopeTolerance>
|
||||||
|
<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
|
||||||
|
<DeNovoTolerance>0.02</DeNovoTolerance>
|
||||||
|
<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
|
||||||
|
<Deisotope>True</Deisotope>
|
||||||
|
<Topx>10</Topx>
|
||||||
|
<TopxInterval>100</TopxInterval>
|
||||||
|
<HigherCharges>True</HigherCharges>
|
||||||
|
<IncludeWater>True</IncludeWater>
|
||||||
|
<IncludeAmmonia>True</IncludeAmmonia>
|
||||||
|
<DependentLosses>True</DependentLosses>
|
||||||
|
<Recalibration>False</Recalibration>
|
||||||
|
</msmsParams>
|
||||||
|
<msmsParams>
|
||||||
|
<Name>Unknown</Name>
|
||||||
|
<MatchTolerance>20</MatchTolerance>
|
||||||
|
<MatchToleranceInPpm>True</MatchToleranceInPpm>
|
||||||
|
<DeisotopeTolerance>7</DeisotopeTolerance>
|
||||||
|
<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
|
||||||
|
<DeNovoTolerance>10</DeNovoTolerance>
|
||||||
|
<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
|
||||||
|
<Deisotope>True</Deisotope>
|
||||||
|
<Topx>12</Topx>
|
||||||
|
<TopxInterval>100</TopxInterval>
|
||||||
|
<HigherCharges>True</HigherCharges>
|
||||||
|
<IncludeWater>True</IncludeWater>
|
||||||
|
<IncludeAmmonia>True</IncludeAmmonia>
|
||||||
|
<DependentLosses>True</DependentLosses>
|
||||||
|
<Recalibration>False</Recalibration>
|
||||||
|
</msmsParams>
|
||||||
|
</msmsParamsArray>
|
||||||
|
<fragmentationParamsArray>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>CID</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>HCD</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>ETD</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>PQD</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>ETHCD</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>ETCID</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>UVPD</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
<fragmentationParams>
|
||||||
|
<Name>Unknown</Name>
|
||||||
|
<Connected>False</Connected>
|
||||||
|
<ConnectedScore0>1</ConnectedScore0>
|
||||||
|
<ConnectedScore1>1</ConnectedScore1>
|
||||||
|
<ConnectedScore2>1</ConnectedScore2>
|
||||||
|
<InternalFragments>False</InternalFragments>
|
||||||
|
<InternalFragmentWeight>1</InternalFragmentWeight>
|
||||||
|
<InternalFragmentAas>KRH</InternalFragmentAas>
|
||||||
|
</fragmentationParams>
|
||||||
|
</fragmentationParamsArray>
|
||||||
|
</MaxQuantParams>
|
||||||
10
tests/modules/maxquant/lfq/test.yml
Normal file
10
tests/modules/maxquant/lfq/test.yml
Normal file
|
|
@ -0,0 +1,10 @@
|
||||||
|
## TODO nf-core: Please run the following command to build this file:
|
||||||
|
# nf-core modules create-test-yml 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
|
||||||
|
tags:
|
||||||
|
- maxquant
|
||||||
|
- maxquant/lfq
|
||||||
|
files:
|
||||||
|
- path: output/maxquant/proteinGroups.txt
|
||||||
|
md5sum: e667c7caad0bc4b7ac383fd023c654fc
|
||||||
57976
tests/modules/maxquant/lfq/yeast.fasta
Normal file
57976
tests/modules/maxquant/lfq/yeast.fasta
Normal file
File diff suppressed because it is too large
Load diff
Loading…
Reference in a new issue