From 2657c360b4e4dfecdbb7670dbd0402529c594596 Mon Sep 17 00:00:00 2001 From: daichengxin <1278747277@qq.com> Date: Tue, 24 May 2022 08:35:26 +0800 Subject: [PATCH 1/3] minor fixed --- bin/diann_convert.py | 1 - conf/test_full_dia.config | 2 +- conf/test_full_lfq.config | 2 +- modules/local/diannsummary/main.nf | 2 +- nextflow.config | 2 +- nextflow_schema.json | 1 + 6 files changed, 5 insertions(+), 5 deletions(-) diff --git a/bin/diann_convert.py b/bin/diann_convert.py index 0d0ae201..659a4463 100755 --- a/bin/diann_convert.py +++ b/bin/diann_convert.py @@ -53,7 +53,6 @@ def convert(ctx, diann_report, exp_design, qvalue_threshold): out_triqler = out_msstats[['ProteinName', 'PeptideSequence', 'PrecursorCharge', 'Intensity', 'Run', 'Condition']] out_triqler.columns = ['proteins', 'peptide', 'charge', 'intensity', 'run', 'condition'] - # https://github.com/statisticalbiotechnology/dia_sum/blob/main/scripts/result_scripts/diann_output_to_triqler_output.py out_triqler.loc[:, "searchScore"] = report['Q.Value'] out_triqler.loc[:, "searchScore"] = -np.log(out_triqler["searchScore"]) diff --git a/conf/test_full_dia.config b/conf/test_full_dia.config index 99598d47..8695aed8 100644 --- a/conf/test_full_dia.config +++ b/conf/test_full_dia.config @@ -2,7 +2,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running real full dia tests (DIA) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple test. + Defines input files and everything required to run a Real and full-size test. Use as follows: nextflow run nf-core/quantms -profile test_full_dia, [--outdir ] diff --git a/conf/test_full_lfq.config b/conf/test_full_lfq.config index d5e69a71..b93f1913 100644 --- a/conf/test_full_lfq.config +++ b/conf/test_full_lfq.config @@ -2,7 +2,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running real full-size tests ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple test. + Defines input files and everything required to run a real and full-size test. Use as follows: nextflow run nf-core/quantms -profile test_full_lfq, [--outdir ] diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf index 980a6555..a326e20d 100644 --- a/modules/local/diannsummary/main.nf +++ b/modules/local/diannsummary/main.nf @@ -44,7 +44,7 @@ process DIANNSUMMARY { --use-quant \\ --matrices \\ --out diann_report.tsv \\ - --qvalue $params.psm_level_fdr_cutoff \\ + --qvalue $params.protein_level_fdr_cutoff \\ $args \\ |& tee diannsummary.log diff --git a/nextflow.config b/nextflow.config index 6e59f03c..e2207d42 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,7 @@ params { // Workflow flags input = null // the sdrf and spectra parameters are inferred from this one root_folder = null - local_input_type = null + local_input_type = 'mzML' database = null acquisition_method = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 2f548135..1de7610d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -46,6 +46,7 @@ "type": "string", "description": "Overwrite the file type/extension of the filename as specified in the SDRF/design", "fa_icon": "fas fa-file-invoice", + "default": "mzML", "help_text": "If the above [`--root_folder`](#root_folder) was given to load local input files, this overwrites the file type/extension of\nthe filename as specified in the SDRF/design. Usually used in case you have an mzML-converted version of the files already. Needs to be\none of 'mzML' or 'raw' (the letter cases should match your files exactly)." } } From 96f1a174aefc7ecadc138755ba457bf7b07ffab4 Mon Sep 17 00:00:00 2001 From: daichengxin <1278747277@qq.com> Date: Tue, 24 May 2022 08:40:30 +0800 Subject: [PATCH 2/3] update --- conf/test_full_dia.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full_dia.config b/conf/test_full_dia.config index 8695aed8..6c4f68f9 100644 --- a/conf/test_full_dia.config +++ b/conf/test_full_dia.config @@ -2,7 +2,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running real full dia tests (DIA) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a Real and full-size test. + Defines input files and everything required to run a real and full-size test. Use as follows: nextflow run nf-core/quantms -profile test_full_dia, [--outdir ] From 33dfebc5e9e113eea17dc5c9c2f3a1e7b3a06bab Mon Sep 17 00:00:00 2001 From: daichengxin <1278747277@qq.com> Date: Tue, 24 May 2022 09:01:31 +0800 Subject: [PATCH 3/3] fixed --- subworkflows/local/create_input_channel.nf | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/create_input_channel.nf b/subworkflows/local/create_input_channel.nf index 93109b8e..e875b12d 100644 --- a/subworkflows/local/create_input_channel.nf +++ b/subworkflows/local/create_input_channel.nf @@ -79,11 +79,12 @@ def create_meta_channel(LinkedHashMap row, is_sdrf, enzymes, files, wrapper) { // apply transformations given by specified root_folder and type if (params.root_folder) { filestr = params.root_folder + File.separator + filestr - } - - filestr = (params.local_input_type ? filestr.take(filestr.lastIndexOf('.')) + filestr = (params.local_input_type ? filestr.take(filestr.lastIndexOf('.')) + '.' + params.local_input_type : filestr) + } + + // existance check if (!file(filestr).exists()) {