Handling DIANN parameters to get extended parameters to modules validated

.github/workflows/ci.yml

@@ -39,6 +39,7 @@ jobs:
           [
             "test_lfq",
             "test_dia",
+            "test_dia_dotd",
             "test_localize",
             "test_tmt",
             "test_dda_id_alphapeptdeep",

.github/workflows/extended_ci.yml

@@ -34,6 +34,7 @@ jobs:
           [
             "test_lfq",
             "test_dia",
+            "test_dia_dotd",
             "test_localize",
             "test_tmt",
             "test_dda_id_alphapeptdeep",
@@ -126,6 +127,7 @@ jobs:
           [
             "test_lfq",
             "test_dia",
+            "test_dia_dotd",
             "test_localize",
             "test_tmt",
             "test_dda_id_ms2pip",

.gitignore

@@ -16,3 +16,10 @@ null/
 #Ignore cursor AI rules
 .cursor/rules/codacy.mdc
 .codacy/
+
+# Claude Code
+.claude/
+
+
+#Ignore vscode AI rules
+.github/instructions/codacy.instructions.md

.nf-core.yml

@@ -23,7 +23,7 @@ lint:
   modules_config: false
   multiqc_config: false
   nextflow_config: false
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Yasset Perez-Riverol

CHANGELOG.md

@@ -298,8 +298,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [1.0] nfcore/quantms - [05/02/2022] - Havana
 
-Initial release of bigbio/quantms, created with the [nf-core](https://nf-co.re/) template.
-
 ### `Added`
 
 - New pipeline for DDA-LFQ data analysis

CITATIONS.md

@@ -66,10 +66,6 @@
 
   > Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY: A Method for Efficient High-Confidence Protein Inference. J Proteome Res. 2020 Mar 6;19(3):1060-1072. doi: 10.1021/acs.jproteome.9b00566. Epub 2020 Feb 13. PMID: 31975601; PMCID: PMC7583457.
 
-- [Triqler](https://pubmed.ncbi.nlm.nih.gov/30482846/)
-
-  > The M, Käll L. Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics. Mol Cell Proteomics. 2019 Mar;18(3):561-570. doi: 10.1074/mcp.RA118.001018. Epub 2018 Nov 27. PMID: 30482846; PMCID: PMC6398204.
-
 - [luciphor](https://pubmed.ncbi.nlm.nih.gov/23918812/)
 
   > Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5. PMID: 23918812; PMCID: PMC3820951.

README.md

@@ -7,7 +7,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/quantms)

conf/modules/dia.config

@@ -0,0 +1,32 @@
+/*
+========================================================================================
+    DIA-NN module options — all DIA pipeline steps
+========================================================================================
+    Passes params.diann_extra_args to each DIA-NN step via ext.args.
+    Blocked-flag validation is performed in each module's script block,
+    so it applies regardless of whether ext.args is overridden by the user.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    withName: ".*:DIA:INSILICO_LIBRARY_GENERATION" {
+        ext.args   = { params.diann_extra_args ?: '' }
+    }
+
+    withName: ".*:DIA:PRELIMINARY_ANALYSIS" {
+        ext.args   = { params.diann_extra_args ?: '' }
+    }
+
+    withName: ".*:DIA:ASSEMBLE_EMPIRICAL_LIBRARY" {
+        ext.args   = { params.diann_extra_args ?: '' }
+    }
+
+    withName: ".*:DIA:INDIVIDUAL_ANALYSIS" {
+        ext.args   = { params.diann_extra_args ?: '' }
+    }
+
+    withName: ".*:DIA:FINAL_QUANTIFICATION" {
+        ext.args   = { params.diann_extra_args ?: '' }
+    }
+}

conf/modules/id.config

@@ -0,0 +1,77 @@
+/*
+========================================================================================
+    ID/PSM processing module options — shared across DDA workflows
+========================================================================================
+*/
+
+process {
+
+    // FDRCONSENSUSID
+    withName: '.*:FDR_CONSENSUSID' {
+        ext.args    = "-PSM true -protein false"
+    }
+
+    // ID_SCORE_SWITCHER for phospho scoring
+    withName: '.*:ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
+        ext.args    = [
+            "-new_score_orientation lower_better",
+            "-old_score \"q-value\"",
+            "-new_score_type \"Posterior Error Probability\"",
+            "-debug $params.idscoreswitcher_debug"
+        ].join(' ').trim()
+    }
+
+    // ONSITE phospho scoring
+    withName: '.*:ID:PHOSPHO_SCORING:ONSITE' {
+        ext.args    = "-debug $params.onsite_debug"
+    }
+
+    // PERCOLATOR
+    withName: '.*:PERCOLATOR' {
+        ext.args    = [
+            "-debug $params.percolator_debug",
+            (params.fdr_level != 'psm_level_fdrs') ? "-" + params.fdr_level : ""
+        ].join(' ').trim()
+    }
+
+    // EPIFANY
+    withName: '.*:PROTEIN_INFERENCE_EPIFANY' {
+        ext.args    = "-keep_best_psm_only false -debug $params.protein_inference_debug"
+    }
+
+    // PROTEIN_INFERENCE (generic)
+    withName: '.*:PROTEIN_INFERENCE' {
+        ext.args    = "-debug $params.protein_inference_debug"
+    }
+
+    // PSM FDR control ID_FILTER
+    withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
+        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
+        ext.suffix  = '.idXML'
+    }
+
+    // DDA_ID PSM FDR control ID_FILTER
+    withName: '.*:DDA_ID:PSM_FDR_CONTROL:ID_FILTER' {
+        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
+        ext.suffix  = '.idXML'
+    }
+
+    // MS2RESCORE
+    withName: 'MSRESCORE_FEATURES' {
+        ext.args   = [
+            "--ms2_model ${params.ms2features_model}",
+            "--calibration_set_size ${params.ms2features_calibration}",
+            params.ms2features_generators.trim() ? "--feature_generators ${params.ms2features_generators}" : ''
+        ].join(' ').trim()
+    }
+
+    // DDA_ID phospho scoring ID_SCORE_SWITCHER
+    withName: '.*:DDA_ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
+        ext.args   = [
+            "-new_score_orientation lower_better",
+            "-old_score \"q-value\"",
+            "-new_score_type \"Posterior Error Probability\"",
+            "-debug $params.idscoreswitcher_debug"
+        ].join(' ').trim()
+    }
+}

conf/modules/lfq.config

@@ -0,0 +1,13 @@
+/*
+========================================================================================
+    LFQ module options — LFQ-specific processes
+========================================================================================
+*/
+
+process {
+
+    // PROTEOMICSLFQ
+    withName: '.*:LFQ:PROTEOMICSLFQ' {
+        ext.args    = "-debug $params.plfq_debug"
+    }
+}