Merge pull request #208 from daichengxin/dev

update pmultiqc

Author: ypriverol

modules/local/openms/thirdparty/searchenginemsgf/main.nf

@@ -75,7 +75,7 @@ process SEARCHENGINEMSGF {
         -min_peptide_length $params.min_peptide_length \\
         -max_peptide_length $params.max_peptide_length \\
         -isotope_error_range $params.isotope_error_range \\
-        -enzyme ${enzyme} \\
+        -enzyme "${enzyme}" \\
         -tryptic ${msgf_num_enzyme_termini} \\
         -precursor_mass_tolerance $meta.precursormasstolerance \\
         -precursor_error_units $meta.precursormasstoleranceunit \\

modules/local/pmultiqc/main.nf

@@ -1,11 +1,11 @@
 process PMULTIQC {
     label 'process_high'
 
-    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.12" : null)
+    conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.13" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.12--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.13--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.12--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.13--pyhdfd78af_0"
     }
 
     input:
@@ -22,13 +22,16 @@ process PMULTIQC {
     script:
     def args = task.ext.args ?: ''
     def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "" : "--disable_plugin"
+    def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable_table" : ""
 
     """
     multiqc \\
         -f \\
         --config ./results/multiqc_config.yml \\
         ${args} \\
         ${disable_pmultiqc} \\
+        ${disable_table_plots} \\
+        --quantification_method $params.quantification_method \\
         ./results \\
         -o .
 

nextflow.config

@@ -191,6 +191,7 @@ params {
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
+    skip_table_plots           = false
     max_multiqc_email_size     = '25.MB'
 
     // Boilerplate options

nextflow_schema.json

@@ -1182,6 +1182,12 @@
                     "fa_icon": "fas fa-cog",
                     "hidden": true
                 },
+                "skip_table_plots": {
+                    "type": "boolean",
+                    "description": "Skip protein/peptide table plots with pmultiqc for large dataset.",
+                    "fa_icon": "fas fa-toggle-on",
+                    "default": false
+                },
                 "tracedir": {
                     "type": "string",
                     "description": "Directory to keep pipeline Nextflow logs and reports.",

workflows/quantms.nf

@@ -182,7 +182,7 @@ workflow QUANTMS {
             .combine(ch_pipeline_results.ifEmpty([]).combine(ch_multiqc_files.collect())
             .combine(ch_pmultiqc_mzmls.collect())
             .combine(ch_ids_pmultiqc.collect().ifEmpty([])))
-            .combine(ch_msstats_in),
+            .combine(ch_msstats_in.ifEmpty([])),
         ch_multiqc_quantms_logo
     )
     multiqc_report      = SUMMARYPIPELINE.out.ch_pmultiqc_report.toList()