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Merge pull request #349 from jonasscheid/generate_speclib
Generate spectrum library using EasyPQP
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/mhcquant -profile test,<docker/singularity> --outdir <OUTDIR> | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| resourceLimits = [ | ||
| cpus: 2, | ||
| memory: '6.GB', | ||
| time: '2.h' | ||
| ] | ||
| } | ||
|
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| params { | ||
| config_profile_name = 'Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function' | ||
|
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| // Input data | ||
| input = params.pipelines_testdata_base_path + 'mhcquant/testdata/HepG2_sample_sheet.tsv' | ||
| fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta' | ||
| generate_speclib = true | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| process EASYPQP_CONVERT { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
|
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| conda "bioconda::easypqp=0.1.50" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/easypqp:0.1.50--pyhdfd78af_1' : | ||
| 'biocontainers/easypqp:0.1.50--pyhdfd78af_1' }" | ||
|
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| input: | ||
| tuple val(meta), path(pepxml), path(spectra) | ||
| path unimod | ||
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| output: | ||
| tuple val(meta), path("*.psmpkl") , emit: psmpkl | ||
| tuple val(meta), path("*.peakpkl"), emit: peakpkl | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
|
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| """ | ||
| export MPLCONFIGDIR=/tmp/matplotlib | ||
| export XDG_CACHE_HOME=/tmp/fontconfig-cache | ||
| mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME | ||
| easypqp convert \\ | ||
| --pepxml $pepxml \\ | ||
| --spectra $spectra \\ | ||
| --unimod $unimod \\ | ||
| $args | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| """ | ||
| export MPLCONFIGDIR=/tmp/matplotlib | ||
| export XDG_CACHE_HOME=/tmp/fontconfig-cache | ||
| mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME | ||
| touch "${prefix}.psmpkl" | ||
| touch "${prefix}.peakpkl" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| process EASYPQP_LIBRARY { | ||
| tag "$meta.id" | ||
| label 'process_single' | ||
|
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| conda "bioconda::easypqp=0.1.50" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/easypqp:0.1.50--pyhdfd78af_1' : | ||
| 'biocontainers/easypqp:0.1.50--pyhdfd78af_1' }" | ||
|
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| input: | ||
| tuple val(meta), path(psmpkl), path(peakpkl) | ||
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| output: | ||
| tuple val(meta), path("*.tsv") , emit: tsv | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
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| """ | ||
| export MPLCONFIGDIR=/tmp/matplotlib | ||
| export XDG_CACHE_HOME=/tmp/fontconfig-cache | ||
| mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME | ||
| easypqp library \ | ||
| --out ${prefix}_speclib.tsv \ | ||
| $args \ | ||
| $psmpkl $peakpkl | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') | ||
| END_VERSIONS | ||
| """ | ||
|
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
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| """ | ||
| export MPLCONFIGDIR=/tmp/matplotlib | ||
| export XDG_CACHE_HOME=/tmp/fontconfig-cache | ||
| mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME | ||
| touch "${prefix}_speclib.tsv" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| /* | ||
| * Generates spectrum library for DIA-based searches | ||
| */ | ||
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| // | ||
| // MODULE: Loaded from modules/local/ | ||
| // | ||
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| include { EASYPQP_CONVERT } from '../../modules/local/easypqp/convert' | ||
| include { EASYPQP_LIBRARY; | ||
| EASYPQP_LIBRARY as EASYPQP_LIBRARY_GLOBAL } from '../../modules/local/easypqp/library' | ||
|
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| // | ||
| // MODULE: Installed directly from nf-core/modules | ||
| // | ||
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| workflow SPECLIB { | ||
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| take: | ||
| fdrfiltered_comet_idxml | ||
| mzml | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
|
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| // Load unimod tables (Future:) | ||
| unimod = file("$projectDir/assets/250120_unimod_tables.xml", checkIfExists: true) | ||
|
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| // Convert psms and spectra to pickle files | ||
| EASYPQP_CONVERT(fdrfiltered_comet_idxml.join(mzml), unimod) | ||
| ch_versions = ch_versions.mix(EASYPQP_CONVERT.out.versions) | ||
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| EASYPQP_CONVERT.out.psmpkl | ||
| .map { meta, psmpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), psmpkl] } | ||
| .groupTuple() | ||
| .set { ch_psmpkl } | ||
| EASYPQP_CONVERT.out.peakpkl | ||
| .map { meta, peakpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), peakpkl] } | ||
| .groupTuple() | ||
| .set { ch_peakpkl } | ||
|
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| // Generate spectrum library for each sample-condition pair | ||
| EASYPQP_LIBRARY(ch_psmpkl.join(ch_peakpkl)) | ||
| ch_versions = ch_versions.mix(EASYPQP_LIBRARY.out.versions) | ||
|
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| // Generate spectrum library for all MSruns in the samplesheet | ||
| if (params.global_fdr) { | ||
| EASYPQP_CONVERT.out.psmpkl | ||
| .map { meta, psmpkl -> [[id: "global"], psmpkl] } | ||
| .groupTuple() | ||
| .set { ch_global_psmpkl } | ||
| EASYPQP_CONVERT.out.peakpkl | ||
| .map { meta, peakpkl -> [[id: "global"], peakpkl] } | ||
| .groupTuple() | ||
| .set { ch_global_peakpkl } | ||
| EASYPQP_LIBRARY_GLOBAL(ch_global_psmpkl.join(ch_global_peakpkl)) | ||
| } | ||
|
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| emit: | ||
| versions = ch_versions | ||
| } |
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