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[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. #187

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merged 4 commits into from
May 20, 2022
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[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. #187

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6ad3187
[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly chan…
jpfeuffer May 20, 2022
99ba1bf
major fix. before inference FDR always has to be PSM
jpfeuffer May 20, 2022
35316a0
Disable protein FDR before inference
jpfeuffer May 20, 2022
bc65327
Set protein FDR in localize back to 0.05
jpfeuffer May 20, 2022
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20 changes: 18 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,20 @@ if (params.enable_mod_localization) {
}
}

process {
// FDRCONSENSUSID
withName: '.*:FDRCONSENSUSID' {
ext.args = "-PSM true"
}
}

process {
// FDRIDPEP
withName: '.*:FDRIDPEP' {
ext.args = "-PSM true"
}
}

process {
// ISOBARICANALYZER
withName: '.*:TMT:.*:ISOBARICANALYZER' {
Expand All @@ -161,9 +175,11 @@ process {
}

// IDFILTER on PROTEIN LEVEL
level = params.protein_quant == 'strictly_unique_peptides' ? 'prot' : 'protgroup'
withName: '.*:TMT:PROTEININFERENCE:IDFILTER' {
ext.args = [
"-score:prot \"$params.protein_level_fdr_cutoff\"",
"-score:${level} \"$params.protein_level_fdr_cutoff\"",
"-score:pep \"$params.psm_level_fdr_cutoff\"",
"-delete_unreferenced_peptide_hits",
"-remove_decoys"
].join(' ').trim()
Expand Down Expand Up @@ -218,7 +234,7 @@ process {

// IDFILTER
withName: '.*:ID:PSMFDRCONTROL:IDFILTER' {
ext.args = "-score:pep \"$params.psm_pep_fdr_cutoff\""
ext.args = "-score:pep \"$params.run_fdr_cutoff\""
ext.suffix = '.idXML'
publishDir = [
path: { "${params.outdir}/idfilter" },
Expand Down
1 change: 1 addition & 0 deletions conf/test_lfq.config
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Expand Up @@ -32,5 +32,6 @@ params {
enable_qc = true
add_triqler_output = true
protein_level_fdr_cutoff = 1.0
psm_level_fdr_cutoff = 1.0
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@jpfeuffer why this is 1.0 and not 0.01

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To bem backwards compatible in the tests. This has so few peptides that it might fail.

acquisition_method = "dda"
}
1 change: 1 addition & 0 deletions conf/test_localize.config
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Expand Up @@ -28,5 +28,6 @@ params {
enable_mod_localization = true
search_engines = 'comet,msgf'
enable_qc = true
psm_level_fdr_cutoff = 1.0
skip_post_msstats = true
}
3 changes: 1 addition & 2 deletions conf/test_tmt.config
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Expand Up @@ -28,8 +28,7 @@ params {
database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/erwinia_carotovora.fasta'
posterior_probabilities = "percolator"
search_engines = "comet,msgf"
protein_level_fdr_cutoff = 0.01
psm_pep_fdr_cutoff = 0.01
psm_level_fdr_cutoff = 1.0
decoy_affix = "rev"
label = 'tmt6plex'
fragment_method = 'HCD'
Expand Down
1 change: 0 additions & 1 deletion modules/local/openms/falsediscoveryrate/main.nf
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Expand Up @@ -26,7 +26,6 @@ process FALSEDISCOVERYRATE {
-in ${id_file} \\
-out ${id_file.baseName}_fdr.idXML \\
-threads $task.cpus \\
-protein $params.protein \\
-algorithm:add_decoy_peptides \\
-algorithm:add_decoy_proteins \\
$args \\
Expand Down
11 changes: 6 additions & 5 deletions modules/local/openms/proteomicslfq/main.nf
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Expand Up @@ -35,6 +35,7 @@ process PROTEOMICSLFQ {

"""
ProteomicsLFQ \\
-threads ${task.cpus} \\
-in ${(mzmls as List).join(' ')} \\
-ids ${(id_files as List).join(' ')} \\
-design ${expdes} \\
Expand All @@ -46,14 +47,14 @@ process PROTEOMICSLFQ {
-transfer_ids ${params.transfer_ids} \\
-protein_quantification ${params.protein_quant} \\
-alignment_order ${params.alignment_order} \\
-picked_proteinFDR true \\
${decoys_present} \\
-psmFDR ${params.psm_level_fdr_cutoff} \\
-proteinFDR ${params.protein_level_fdr_cutoff} \\
-picked_proteinFDR ${params.picked_fdr} \\
-out_cxml ${expdes.baseName - ~/_design$/}.consensusXML \\
-out ${expdes.baseName - ~/_design$/}.mzTab \\
-threads ${task.cpus} \\
${msstats_present} \\
${triqler_present} \\
${decoys_present} \\
-out_cxml ${expdes.baseName - ~/_design$/}.consensusXML \\
-proteinFDR ${params.protein_level_fdr_cutoff} \\
$args \\
|& tee proteomicslfq.log
Expand Down
8 changes: 3 additions & 5 deletions nextflow.config
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Expand Up @@ -21,8 +21,9 @@ params {
add_decoys = false
enable_pmultiqc = true
search_engines = 'comet'
psm_pep_fdr_cutoff = 0.10
protein_level_fdr_cutoff = 0.05
run_fdr_cutoff = 0.10
protein_level_fdr_cutoff = 0.01
psm_level_fdr_cutoff = 0.01

// Debug level
decoydatabase_debug = 0
Expand Down Expand Up @@ -93,9 +94,6 @@ params {
// IDPEP flags
outlier_handling = "none"

// Falsediscoveryrate
protein = false

// Percolator flags
train_FDR = 0.05
test_FDR = 0.05
Expand Down
223 changes: 112 additions & 111 deletions nextflow_schema.json
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