Merge pull request #187 from nf-core/fix/FDRusageAndNaming

[FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage.
bigbio · May 20, 2022 · 15a5379 · 15a5379
2 parents 462deea + bc65327
commit 15a5379
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Showing 8 changed files with 143 additions and 126 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -137,6 +137,20 @@ if (params.enable_mod_localization) {
     }
 }
 
+process {
+    // FDRCONSENSUSID
+    withName: '.*:FDRCONSENSUSID' {
+        ext.args    = "-PSM true -protein false"
+    }
+}
+
+process {
+    // FDRIDPEP
+    withName: '.*:FDRIDPEP' {
+        ext.args    = "-PSM true -protein false"
+    }
+}
+
 process {
     // ISOBARICANALYZER
     withName: '.*:TMT:.*:ISOBARICANALYZER' {
@@ -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()
@@ -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" },

diff --git a/conf/test_lfq.config b/conf/test_lfq.config
@@ -32,5 +32,6 @@ params {
     enable_qc = true
     add_triqler_output = true
     protein_level_fdr_cutoff = 1.0
+    psm_level_fdr_cutoff = 1.0
     acquisition_method = "dda"
 }
diff --git a/conf/test_localize.config b/conf/test_localize.config
@@ -28,5 +28,7 @@ params {
     enable_mod_localization = true
     search_engines = 'comet,msgf'
     enable_qc = true
+    protein_level_fdr_cutoff = 0.05
+    psm_level_fdr_cutoff = 1.0
     skip_post_msstats = true
 }
diff --git a/conf/test_tmt.config b/conf/test_tmt.config
@@ -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'

diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf
@@ -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 \\

diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
@@ -35,6 +35,7 @@ process PROTEOMICSLFQ {
 
     """
     ProteomicsLFQ \\
+        -threads ${task.cpus} \\
         -in ${(mzmls as List).join(' ')} \\
         -ids ${(id_files as List).join(' ')} \\
         -design ${expdes} \\
@@ -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
 

diff --git a/nextflow.config b/nextflow.config
@@ -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
@@ -93,9 +94,6 @@ params {
     // IDPEP flags
     outlier_handling = "none"
 
-    // Falsediscoveryrate
-    protein = false
-
     // Percolator flags
     train_FDR                    = 0.05
     test_FDR                     = 0.05

diff --git a/nextflow_schema.json b/nextflow_schema.json