Remove unused logo

assets/multiqc_config.yml

@@ -1,79 +1,14 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/bigbio/quantmsdiann/tree/dev" target="_blank">bigbio/quantmsdiann</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://docs.quantms.org/en/latest" target="_blank">documentation</a>.
-report_section_order:
-  pmultiqc:
-    order: 1000
-  "nf-core-quantms-methods-description":
-    order: -1000
-  software_versions:
-    order: -1001
-  "bigbio-quantmsdiann-summary":
-    order: -1002
 
 thousandsSep_format: ","
 export_plots: false
 
-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"
   pmultiqc/exp_design:
     fn: "*_design.tsv"
   pmultiqc/sdrf:
     fn: "*.sdrf.tsv"
-  pmultiqc/mztab:
-    fn: "*.mzTab"
-    num_lines: 0
-  pmultiqc/mzML:
-    fn: "*.mzML"
-    num_lines: 0
-  pmultiqc/ms_info:
-    fn: "*_ms_info.parquet"
-    num_lines: 0
-  pmultiqc/idXML:
-    fn: "*.idXML"
-    num_lines: 0
   pmultiqc/msstats:
     fn: "*msstats_in.csv"
     num_lines: 0

modules/local/pmultiqc/main.nf

@@ -7,7 +7,6 @@ process PMULTIQC {
 
     input:
     path multiqc_inputs, stageAs: 'results/*'
-    path quantms_log
 
     output:
     path "*.html", emit: ch_pmultiqc_report

workflows/quantmsdiann.nf

@@ -114,7 +114,6 @@ workflow QUANTMSDIANN {
     ch_multiqc_files = ch_multiqc_files.mix(DIA.out.diann_log)
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
-    ch_multiqc_quantms_logo = file("${projectDir}/assets/nf-core-quantmsdiann_logo_light.png")
 
     // create cross product of all inputs
     multiqc_inputs = CREATE_INPUT_CHANNEL.out.ch_expdesign
@@ -125,10 +124,7 @@ workflow QUANTMSDIANN {
         .mix(ch_msstats_in.ifEmpty([]))
         .collect()
 
-    SUMMARY_PIPELINE(
-        multiqc_inputs,
-        ch_multiqc_quantms_logo,
-    )
+    SUMMARY_PIPELINE(multiqc_inputs)
 
     emit:
     multiqc_report = SUMMARY_PIPELINE.out.ch_pmultiqc_report.toList()