From fef3595027c50723e0d88ed4172e318d2090f256 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 16:45:22 +0000 Subject: [PATCH 1/7] pmultiqc 0.0.25 --- modules/local/openms/thirdparty/searchenginesage/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index 8257b801..89150ca1 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,6 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ + -charge "$params.min_precursor_charge $params.max_precursor_charge" \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From 0dc94b507ee81f276de375fc01686b1c52f18e68 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 16:54:23 +0000 Subject: [PATCH 2/7] SAGE charges --- modules/local/openms/thirdparty/searchenginesage/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index 89150ca1..db1e4277 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,7 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ - -charge "$params.min_precursor_charge $params.max_precursor_charge" \\ + -charges "$params.min_precursor_charge $params.max_precursor_charge" \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From 3bf668d1a9f70a86682815d2494226f56a806fb9 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 17:03:55 +0000 Subject: [PATCH 3/7] SAGE charges --- modules/local/openms/thirdparty/searchenginesage/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index db1e4277..ba512f4f 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,7 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ - -charges "$params.min_precursor_charge $params.max_precursor_charge" \\ + -charges "[$params.min_precursor_charge $params.max_precursor_charge]" \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From 4549fb8068c50d5e549b674c54cba9bebc6e6f3f Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 20:35:45 +0000 Subject: [PATCH 4/7] SAGE charges --- modules/local/openms/thirdparty/searchenginesage/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index ba512f4f..89efcf85 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,7 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ - -charges "[$params.min_precursor_charge $params.max_precursor_charge]" \\ + -charges '[$params.min_precursor_charge $params.max_precursor_charge]' \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From 25b28f852a8fb0feb3dbad6f444064576465ee21 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 20:47:57 +0000 Subject: [PATCH 5/7] SAGE charges --- modules/local/openms/thirdparty/searchenginesage/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index 89efcf85..db1e4277 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,7 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ - -charges '[$params.min_precursor_charge $params.max_precursor_charge]' \\ + -charges "$params.min_precursor_charge $params.max_precursor_charge" \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From a003f4b4b24a58c6702d3e996a8316bf5634e96f Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 25 Mar 2024 20:57:13 +0000 Subject: [PATCH 6/7] SAGE charges --- modules/local/openms/thirdparty/searchenginesage/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index db1e4277..f88f82b2 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -50,7 +50,7 @@ process SEARCHENGINESAGE { -fragment_tol_unit $meta.fragmentmasstoleranceunit \\ -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ - -charges "$params.min_precursor_charge $params.max_precursor_charge" \\ + -charges "$params.min_precursor_charge, $params.max_precursor_charge" \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ From 6a5e3195e3cd4b6661e6256c1e05dd18af672403 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 26 Mar 2024 06:19:22 +0000 Subject: [PATCH 7/7] added min number of peaks per spectrum --- modules/local/openms/thirdparty/searchenginecomet/main.nf | 1 + modules/local/openms/thirdparty/searchenginesage/main.nf | 1 + nextflow.config | 1 + nextflow_schema.json | 7 +++++++ 4 files changed, 10 insertions(+) diff --git a/modules/local/openms/thirdparty/searchenginecomet/main.nf b/modules/local/openms/thirdparty/searchenginecomet/main.nf index a9b35c2a..b8f1a91a 100644 --- a/modules/local/openms/thirdparty/searchenginecomet/main.nf +++ b/modules/local/openms/thirdparty/searchenginecomet/main.nf @@ -102,6 +102,7 @@ process SEARCHENGINECOMET { -precursor_error_units $meta.precursormasstoleranceunit \\ -fragment_mass_tolerance ${bin_tol} \\ -fragment_bin_offset ${bin_offset} \\ + -minimum_peaks $params.min_peaks \\ ${il_equiv} \\ -PeptideIndexing:unmatched_action ${params.unmatched_action} \\ -debug $params.db_debug \\ diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf index f88f82b2..3e6023bc 100644 --- a/modules/local/openms/thirdparty/searchenginesage/main.nf +++ b/modules/local/openms/thirdparty/searchenginesage/main.nf @@ -51,6 +51,7 @@ process SEARCHENGINESAGE { -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\ -charges "$params.min_precursor_charge, $params.max_precursor_charge" \\ + -min_peaks $params.min_peaks \\ -max_variable_mods $params.max_mods \\ -isotope_error_range $params.isotope_error_range \\ ${il_equiv} \\ diff --git a/nextflow.config b/nextflow.config index 8cd10ce8..4f937255 100644 --- a/nextflow.config +++ b/nextflow.config @@ -96,6 +96,7 @@ params { max_peptide_length = 40 num_hits = 1 max_mods = 3 + min_peaks = 10 //minimum number of peaks in a spectrum min_pr_mz = null max_pr_mz = null min_fr_mz = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 8375cfa3..544c02dc 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -324,6 +324,13 @@ "default": 3, "fa_icon": "fas fa-sliders-h" }, + "min_peaks": { + "type": "integer", + "description": "Minimum number of peaks in the spectrum to be considered for the search engine. Default: 10", + "default": 10, + "fa_icon": "fas fa-sliders-h" + }, + "min_pr_mz": { "type": "number", "description": "The minimum precursor m/z for the in silico library generation or library-free search",