update pmultiqc

modules/local/openms/idfilter/main.nf

@@ -1,5 +1,4 @@
 process IDFILTER {
-    tag "$meta.id"
 
     label 'process_very_low'
     label 'process_single_thread'

modules/local/pmultiqc/main.nf

@@ -3,34 +3,32 @@ process PMULTIQC {
 
     conda (params.enable_conda ? "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.10" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.10--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.11--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.10--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.11--pyhdfd78af_0"
     }
 
     input:
-    path expdesign
-    path 'mzMLs/*'
     path 'results/*'
-    path 'raw_ids/*'
     path quantms_log
 
     output:
     path "*.html", emit: ch_pmultiqc_report
-    path "*.db", emit: ch_pmultiqc_db
+    path "*.db", optional:true, emit: ch_pmultiqc_db
     path "versions.yml", emit: versions
     path "*_data", emit: data
     path "*_plots", optional:true, emit: plots
 
     script:
     def args = task.ext.args ?: ''
+    def disable_pmultqic = params.enable_pmultiqc ? "": "--disable_plugin"
 
     """
     multiqc \\
-        --exp_design ${expdesign} \\
-        --mzMLs ./mzMLs \\
-        --raw_ids ./raw_ids \\
+        -f \\
         --config ./results/multiqc_config.yml \\
+        ${args} \\
+        ${disable_pmultqic} \\
         ./results \\
         -o .
 

workflows/quantms.nf

@@ -127,9 +127,7 @@ workflow QUANTMS {
     ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null))
 
     DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign)
-
-    // ch_ids_pmultiqc = ch_ids_pmultiqc.mix(DIA.out.ch_pmultiqc_ids)
-    // ch_pipeline_results = ch_pipeline_results.mix(DIA.out.final_result)
+    ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report)
     ch_versions = ch_versions.mix(DIA.out.versions.ifEmpty(null))
 
 
@@ -154,10 +152,10 @@ workflow QUANTMS {
     ch_multiqc_quantms_logo = file("$projectDir/assets/nf-core-quantms_logo_light.png")
 
     SUMMARYPIPELINE (
-        CREATE_INPUT_CHANNEL.out.ch_expdesign,
-        ch_pmultiqc_mzmls.collect(),
-        ch_pipeline_results.combine(ch_multiqc_files.collect()),
-        ch_ids_pmultiqc.collect(),
+        CREATE_INPUT_CHANNEL.out.ch_expdesign
+            .combine(ch_pipeline_results.combine(ch_multiqc_files.collect())
+            .combine(ch_pmultiqc_mzmls.collect())
+            .combine(ch_ids_pmultiqc.collect().ifEmpty([]))),
         ch_multiqc_quantms_logo
     )
     multiqc_report      = SUMMARYPIPELINE.out.ch_pmultiqc_report.toList()