From a4569757fa7495f3a0b039049ffbf274fcf1d778 Mon Sep 17 00:00:00 2001 From: Leon Bichmann Date: Thu, 1 Oct 2020 11:16:06 +0200 Subject: [PATCH 1/4] add new params --- main.nf | 11 +++++++++-- nextflow.config | 2 ++ nextflow_schema.json | 9 +++++++++ 3 files changed, 20 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index c6b5c7b9..932cefd4 100644 --- a/main.nf +++ b/main.nf @@ -35,6 +35,8 @@ def helpMessage() { --use_z_ions [bool] Use z ions for spectral matching in addition --use_a_ions [bool] Use a ions for spectral matching in addition --use_c_ions [bool] Use c ions for spectral matching in addition + --use_NL_ions [bool] Use NL ions for spectral matching in addition + --remove_precursor_peak [bool] Remove the precursor peak from the MS2 spectra --fdr_threshold [int] Threshold for FDR filtering --fdr_level [str] Level of FDR calculation ('peptide-level-fdrs', 'psm-level-fdrs', 'protein-level-fdrs') --digest_mass_range [int] Mass range of peptides considered for matching @@ -187,6 +189,10 @@ params.use_a_ions = false a_ions = params.use_a_ions ? '-use_A_ions true' : '' params.use_c_ions = false c_ions = params.use_c_ions ? '-use_C_ions true' : '' +params.use_NL_ions = false +NL_ions = params.use_NL_ions ? '-use_NL_ions true' : '' +params.remove_precursor_peak = false +rm_precursor = params.remove_precursor_peak ? '-remove_precursor_peak true' : '' params.skip_decoy_generation = false if (params.skip_decoy_generation) { @@ -581,7 +587,6 @@ process db_search_comet { -allowed_missed_cleavages 0 \\ -precursor_charge ${params.prec_charge} \\ -activation_method ${params.activation_method} \\ - -use_NL_ions true \\ -variable_modifications ${params.variable_mods.tokenize(',').collect { "'${it}'" }.join(" ") } \\ -fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")} \\ -enzyme '${params.enzyme}' \\ @@ -589,7 +594,9 @@ process db_search_comet { $a_ions \\ $c_ions \\ $x_ions \\ - $z_ions \\ + $z_ions \\ + $NL_ions \\ + $rm_precursor \\ """ } diff --git a/nextflow.config b/nextflow.config index e60b4e5c..27ce105e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -75,6 +75,8 @@ params { use_z_ions = false use_a_ions = false use_c_ions = false + use_NL_ions = false + remove_precursor_peak = false skip_quantification = false quantification_fdr = false diff --git a/nextflow_schema.json b/nextflow_schema.json index b077d8c1..3704c4cf 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -181,6 +181,15 @@ "type": "boolean", "description": "Include c ions into the peptide spectrum matching" }, + "use_NL_ions": { + "type": "boolean", + "description": "Include NL ions into the peptide spectrum matching" + }, + "remove_precursor_peak": { + "type": "boolean", + "description": "Include precursor ions into the peptide spectrum matching", + "default": true + }, "spectrum_batch_size": { "type": "integer", "default": 500, From fb63733d1a650245b66d63d92c5581cca9413e7b Mon Sep 17 00:00:00 2001 From: Leon Bichmann Date: Thu, 1 Oct 2020 11:18:45 +0200 Subject: [PATCH 2/4] NL ions to true --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 27ce105e..59173267 100644 --- a/nextflow.config +++ b/nextflow.config @@ -75,7 +75,7 @@ params { use_z_ions = false use_a_ions = false use_c_ions = false - use_NL_ions = false + use_NL_ions = true remove_precursor_peak = false skip_quantification = false quantification_fdr = false From b409290d29bbe7422f43ea7f5ec784304d9cc989 Mon Sep 17 00:00:00 2001 From: Leon Bichmann Date: Thu, 1 Oct 2020 15:17:45 +0200 Subject: [PATCH 3/4] use NL ions false --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 59173267..27ce105e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -75,7 +75,7 @@ params { use_z_ions = false use_a_ions = false use_c_ions = false - use_NL_ions = true + use_NL_ions = false remove_precursor_peak = false skip_quantification = false quantification_fdr = false From 5351674ed31f587d80d31ccf95185dd658ed75c2 Mon Sep 17 00:00:00 2001 From: Leon Bichmann Date: Fri, 2 Oct 2020 09:39:05 +0200 Subject: [PATCH 4/4] rm spaces --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 932cefd4..4ba0a49e 100644 --- a/main.nf +++ b/main.nf @@ -594,9 +594,9 @@ process db_search_comet { $a_ions \\ $c_ions \\ $x_ions \\ - $z_ions \\ + $z_ions \\ $NL_ions \\ - $rm_precursor \\ + $rm_precursor \\ """ }