Feature/bruker data

CHANGELOG.md

@@ -7,10 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Added support for bruker data. And speed-up to DIA-NN pipeline.
+
 ### `Changed`
 
 ### `Fixed`
 
+- Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
+
 ### `Dependencies`
 
 ### `Parameters`

assets/multiqc_config.yml

@@ -18,6 +18,50 @@ custom_logo: "./nf-core-quantms_logo_light.png"
 custom_logo_url: "https://github.com/bigbio/quantms"
 custom_logo_title: "quantms"
 
+custom_data:
+  total_ion_chromatograms:
+    file_format: "tsv"
+    section_name: "MS1 TIC"
+    description: "MS1 total ion chromatograms extracted from the .d files"
+    plot_type: "linegraph"
+    pconfig:
+      id: "ms1_tic"
+      title: "MS1 TIC"
+      ylab: "Ion Count"
+      ymin: 0
+  base_peak_chromatograms:
+    file_format: "tsv"
+    section_name: "MS1 BPC"
+    description: "MS1 base peak chromatograms extracted from the .d files"
+    plot_type: "linegraph"
+    pconfig:
+      id: "ms1_bpc"
+      title: "MS1 BPC"
+      ylab: "Ion Count"
+      ymin: 0
+  number_of_peaks:
+    file_format: "tsv"
+    section_name: "MS1 Peaks"
+    description: "MS1 Peaks from the .d files"
+    plot_type: "linegraph"
+    pconfig:
+      id: "ms1_peaks"
+      title: "MS1 Peaks"
+      ylab: "Peak Count"
+      ymin: 0
+  general_stats:
+    file_format: "tsv"
+    section_name: "General Stats"
+    description: "General stats from the .d files"
+    plot_type: "table"
 sp:
+  total_ion_chromatograms:
+    fn: "tic_*"
+  base_peak_chromatograms:
+    fn: "bpc_*"
+  number_of_peaks:
+    fn: "ms1_peaks_*"
+  general_stats:
+    fn: "general_stats.tsv"
   quantms/exp_design:
     fn: "*_design.tsv"