minor fixed

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"] = 1 - out_triqler["searchScore"]
 

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,<docker/singularity> [--outdir <OUTDIR>]

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,<docker/singularity> [--outdir <OUTDIR>]

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
 

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
 

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)."
                 }
             }

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()) {