multiqc and clean up

Author: yuukiiwa

conf/test_nobc_dx.config

@@ -29,8 +29,6 @@ params {
     fasta               = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_23800000-23980000.fa'
     gtf                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/reference/chr22_23800000-23980000.gtf'
     skip_basecalling    = true
-    skip_nanoplot       = true //remove later
-    skip_alignment      = true //remove later
     run_nanolyse        = true
     protocol            = 'DNA'
     barcode_kit         = 'NBD103/NBD104'

main.nf

@@ -53,8 +53,9 @@ workflow NFCORE_NANOSEQ {
     NANOSEQ ()
     //    samplesheet
     // )
-    //emit:
-    //multiqc_report = NANOSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
+
+    emit:
+    multiqc_report = NANOSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -86,15 +87,15 @@ workflow {
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    //PIPELINE_COMPLETION (
-    //    params.email,
-    //    params.email_on_fail,
-    //    params.plaintext_email,
-    //    params.outdir,
-    //    params.monochrome_logs,
-    //    params.hook_url,
-    //    NFCORE_NANOSEQ.out.multiqc_report
-    //)
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        NFCORE_NANOSEQ.out.multiqc_report
+    )
 }
 
 /*

workflows/nanoseq.nf

@@ -171,11 +171,10 @@ include { QUANTIFY_STRINGTIE_FEATURECOUNTS } from '../subworkflows/local/quantif
 /* --           RUN MAIN WORKFLOW              -- */
 ////////////////////////////////////////////////////
 
-// Info required for completion email and summary
-def multiqc_report      = []
-
 workflow NANOSEQ{
 
+    multiqc_report   = Channel.empty()
+
     // Pre-download test-dataset to get files for '--input_path' parameter
     // Nextflow is unable to recursively download directories via HTTPS
     if (workflow.profile.contains('test') && !workflow.profile.contains('vc')) {
@@ -551,41 +550,25 @@ workflow NANOSEQ{
         ch_software_versions.unique().collectFile()
     )
 
-    //if (!params.skip_multiqc) {
-        // workflow_summary    = WorkflowNanoseq.paramsSummaryMultiqc(workflow, summary_params)
-        // ch_workflow_summary = Channel.value(workflow_summary)
-
+    if (!params.skip_multiqc) {
         /*
          * MODULE: MultiQC
          */
-    //    MULTIQC (
-    //    ch_multiqc_config,
-    //    ch_multiqc_custom_config.collect().ifEmpty([]),
-    //    ch_fastqc_multiqc.ifEmpty([]),
-    //    ch_samtools_multiqc.collect().ifEmpty([]),
-    //    ch_featurecounts_gene_multiqc.ifEmpty([]),
-    //    ch_featurecounts_transcript_multiqc.ifEmpty([]),
-    //    CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
-    //    ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
-    //    )
-    //}
-}
-
-////////////////////////////////////////////////////
-/* --              COMPLETION EMAIL            -- */
-////////////////////////////////////////////////////
+        MULTIQC (
+        ch_multiqc_config,
+        ch_multiqc_custom_config.collect().ifEmpty([]),
+        ch_fastqc_multiqc.ifEmpty([]),
+        ch_samtools_multiqc.collect().ifEmpty([]),
+        ch_featurecounts_gene_multiqc.ifEmpty([]),
+        ch_featurecounts_transcript_multiqc.ifEmpty([]),
+        CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
+        []
+        )
+    }
 
-//workflow.onComplete {
-//    if (params.email) {
-//        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-        //Completion.email(workflow, params, params.summary_params, log, multiqc_report)
-//    }
-//    Completion.summary(workflow, params, log)
-//    NfcoreTemplate.summary(workflow, params, log)
-//    if (params.hook_url) {
-//        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-//    }
-//}
+    emit:
+    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~