From 06623fe24a103a02c21a5bf9d1e1c1290c1b6dcf Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Thu, 28 Nov 2024 14:54:16 +0000 Subject: [PATCH 1/2] IDPEP removed --- modules/local/openms/idpep/main.nf | 37 ---------------------------- modules/local/openms/idpep/meta.yml | 38 ----------------------------- nextflow.config | 5 ---- nextflow_schema.json | 23 ----------------- 4 files changed, 103 deletions(-) delete mode 100644 modules/local/openms/idpep/main.nf delete mode 100644 modules/local/openms/idpep/meta.yml diff --git a/modules/local/openms/idpep/main.nf b/modules/local/openms/idpep/main.nf deleted file mode 100644 index 22eda8e56..000000000 --- a/modules/local/openms/idpep/main.nf +++ /dev/null @@ -1,37 +0,0 @@ -process IDPEP { - tag "$meta.mzml_id" - label 'process_very_low' - label 'openms' - - conda "bioconda::openms-thirdparty=3.2.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.2.0--h9ee0642_4' : - 'biocontainers/openms-thirdparty:3.2.0--h9ee0642_4' }" - - input: - tuple val(meta), path(id_file) - - output: - tuple val(meta), path("${id_file.baseName}_idpep.idXML"), val("q-value_score"), emit: id_files_ForIDPEP - path "versions.yml", emit: versions - path "*.log", emit: log - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.mzml_id}" - - """ - IDPosteriorErrorProbability \\ - -in ${id_file} \\ - -out ${id_file.baseName}_idpep.idXML \\ - -fit_algorithm:outlier_handling $params.outlier_handling \\ - -threads ${task.cpus} \\ - $args \\ - 2>&1 | tee ${id_file.baseName}_idpep.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - IDPosteriorErrorProbability: \$(IDPosteriorErrorProbability 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1) - END_VERSIONS - """ -} diff --git a/modules/local/openms/idpep/meta.yml b/modules/local/openms/idpep/meta.yml deleted file mode 100644 index ba986c8d4..000000000 --- a/modules/local/openms/idpep/meta.yml +++ /dev/null @@ -1,38 +0,0 @@ -name: idpep -description: Tool to estimate the probability of peptide hits to be incorrectly assigned. -keywords: - - PSM rescoring - - decoy - - OpenMS -tools: - - IDPosteriorErrorProbability: - description: | - Tool to estimate the probability of peptide hits to be incorrectly assigned. - homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDPosteriorErrorProbability.html - documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDPosteriorErrorProbability.html -input: - - meta: - type: map - description: Groovy Map containing sample information - - id_file: - type: file - description: | - Identifications from searching a target-decoy database. -output: - - meta: - type: map - description: Groovy Map containing sample information - - id_files_ForIDPEP: - type: file - description: | - Identifications with annotated FDR. - - log: - type: file - description: log file - pattern: "*.log" - - version: - type: file - description: File containing software version - pattern: "versions.yml" -authors: - - "@daichengxin" diff --git a/nextflow.config b/nextflow.config index 2190eea18..41e0fa4aa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -58,8 +58,6 @@ params { shuffle_max_attempts = 30 shuffle_sequence_identity_threshold = 0.5 - // Spectrum pre-processing - //// Peak picking if used openms_peakpicking = false peakpicking_inmemory = false @@ -125,9 +123,6 @@ params { IL_equivalent = true unmatched_action = "warn" - // IDPEP flags - outlier_handling = "none" - // DDA_ID flags export_decoy_psm = true diff --git a/nextflow_schema.json b/nextflow_schema.json index 0482b81cc..8a853caf1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -611,29 +611,6 @@ }, "fa_icon": "fas fa-star-half" }, - "psm_re_scoring_distribution_fitting": { - "title": "PSM re-scoring (distribution fitting)", - "type": "object", - "description": "Use this instead of Percolator if there are problems with Percolator (e.g. due to bad separation) or for performance", - "default": "", - "properties": { - "outlier_handling": { - "type": "string", - "description": "How to handle outliers during fitting:\n\n* ignore_iqr_outliers (default): ignore outliers outside of `3*IQR` from Q1/Q3 for fitting\n* set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting\n* ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem)\n* none: do nothing", - "default": "none", - "fa_icon": "fas fa-list-ol", - "enum": ["none", "ignore_iqr_outliers", "set_iqr_to_closest_valid", "ignore_extreme_percentiles"] - }, - "idpep_debug": { - "type": "integer", - "description": "Debug level for IDPEP step. Increase for verbose logging", - "fa_icon": "fas fa-bug", - "default": 0, - "hidden": true - } - }, - "fa_icon": "far fa-star-half" - }, "consensus_id": { "title": "Consensus ID", "type": "object", From f6f4e47ac47d4d096b13263ff6bbda1f2c8a1653 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Thu, 28 Nov 2024 14:57:08 +0000 Subject: [PATCH 2/2] IDPEP removed --- nextflow_schema.json | 3 --- 1 file changed, 3 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 8a853caf1..b863fae57 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1387,9 +1387,6 @@ { "$ref": "#/$defs/psm_re_scoring_percolator" }, - { - "$ref": "#/$defs/psm_re_scoring_distribution_fitting" - }, { "$ref": "#/$defs/consensus_id" },