From f657b6fe630bf23dc41608a3dafa3eba10c5082f Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 12 Nov 2024 10:59:28 +0000 Subject: [PATCH 1/4] MSstats relaxing thresholds --- nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index ec761e09..6cadbe3c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -211,20 +211,20 @@ params { // MSstats general options - msstats_remove_one_feat_prot = true + msstats_remove_one_feat_prot = false ref_condition = null contrasts = 'pairwise' msstats_threshold = 0.05 skip_post_msstats = false // MSstats LFQ options - msstatslfq_removeFewMeasurements = true + msstatslfq_removeFewMeasurements = false msstatslfq_feature_subset_protein = 'top3' msstatslfq_quant_summary_method = 'TMP' // MSstats ISO options - msstatsiso_useunique_peptide = true - msstatsiso_rmpsm_withfewmea_withinrun = true + msstatsiso_useunique_peptide = false + msstatsiso_rmpsm_withfewmea_withinrun = false msstatsiso_summaryformultiple_psm = 'sum' msstatsiso_summarization_method = 'msstats' msstatsiso_global_norm = true From 230ebff67341ddc4feb5f23f82ab1ac592792526 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 12 Nov 2024 11:12:32 +0000 Subject: [PATCH 2/4] MSstats relaxing thresholds --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 59722a71..ca0d7e82 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1169,19 +1169,19 @@ "type": "boolean", "description": "Omit proteins with only one quantified feature?", "fa_icon": "far fa-check-square", - "default": true + "default": false }, "msstatslfq_removeFewMeasurements": { "type": "boolean", - "description": "Keep features with only one or two measurements across runs?", + "description": "Remove features with only one or two measurements across runs?", "fa_icon": "far fa-check-square", - "default": true + "default": false }, "msstatsiso_useunique_peptide": { "type": "boolean", "description": "Use unique peptide for each protein", "fa_icon": "far fa-check-square", - "default": true + "default": false }, "msstatsiso_rmpsm_withfewmea_withinrun": { "type": "boolean", From f584ec4a0159d5de920596d1e8a00a18dfc328e8 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 12 Nov 2024 11:16:14 +0000 Subject: [PATCH 3/4] increase quantms utils to 0.0.12 --- modules/local/preprocess_expdesign.nf | 4 ++-- modules/local/samplesheet_check.nf | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf index 024b31ad..11114c0a 100644 --- a/modules/local/preprocess_expdesign.nf +++ b/modules/local/preprocess_expdesign.nf @@ -8,8 +8,8 @@ process PREPROCESS_EXPDESIGN { conda "bioconda::quantms-utils=0.0.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }" input: path design diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 02715937..7fd66925 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,8 +5,8 @@ process SAMPLESHEET_CHECK { conda "bioconda::quantms-utils=0.0.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' : - 'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' : + 'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }" input: path input_file From 9bfbca590618c097d9aa22689ee7762a5e6f9760 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 12 Nov 2024 11:27:51 +0000 Subject: [PATCH 4/4] fix default parameters --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index ca0d7e82..432f07f6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1187,7 +1187,7 @@ "type": "boolean", "description": "Remove the features that have 1 or 2 measurements within each run", "fa_icon": "far fa-check-square", - "default": true + "default": false }, "msstatsiso_summaryformultiple_psm": { "type": "string",