Get -profile test running

Author: drpatelh

modules/local/multiqc.nf

@@ -11,6 +11,8 @@ process MULTIQC {
     path multiqc_custom_config
     path software_versions
     path workflow_summary
+    path methods_description
+    path logo
     path fail_trimming_summary
     path fail_mapping_summary
     path fail_strand_check

modules/nf-core/modules/custom/dumpsoftwareversions/main.nf

@@ -130,11 +130,6 @@ include { QUANTIFY_SALMON as QUANTIFY_SALMON      } from '../subworkflows/local/
 //
 // MODULE: Installed directly from nf-core/modules
 //
-<<<<<<< HEAD
-include { FASTQC                      } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
-=======
 include { CAT_FASTQ                   } from '../modules/nf-core/modules/cat/fastq/main'
 include { BBMAP_BBSPLIT               } from '../modules/nf-core/modules/bbmap/bbsplit/main'
 include { SAMTOOLS_SORT               } from '../modules/nf-core/modules/samtools/sort/main'
@@ -144,7 +139,6 @@ include { SORTMERNA                   } from '../modules/nf-core/modules/sortmer
 include { STRINGTIE_STRINGTIE         } from '../modules/nf-core/modules/stringtie/stringtie/main'
 include { SUBREAD_FEATURECOUNTS       } from '../modules/nf-core/modules/subread/featurecounts/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
->>>>>>> origin/dev
 
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -771,30 +765,16 @@ workflow RNASEQ {
         workflow_summary    = WorkflowRnaseq.paramsSummaryMultiqc(workflow, summary_params)
         ch_workflow_summary = Channel.value(workflow_summary)
 
-<<<<<<< HEAD
-    methods_description    = WorkflowRnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
-    ch_methods_description = Channel.value(methods_description)
-
-    ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.collect().ifEmpty([]),
-        ch_multiqc_custom_config.collect().ifEmpty([]),
-        ch_multiqc_logo.collect().ifEmpty([])
-    )
-    multiqc_report = MULTIQC.out.report.toList()
-    ch_versions    = ch_versions.mix(MULTIQC.out.versions)
-=======
+        methods_description    = WorkflowRnaseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+        ch_methods_description = Channel.value(methods_description)
+    
         MULTIQC (
             ch_multiqc_config,
             ch_multiqc_custom_config.collect().ifEmpty([]),
             CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
             ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'),
+            ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'),
+            ch_multiqc_logo.collect().ifEmpty([]),
             ch_fail_trimming_multiqc.ifEmpty([]),
             ch_fail_mapping_multiqc.ifEmpty([]),
             ch_fail_strand_multiqc.ifEmpty([]),
@@ -829,7 +809,6 @@ workflow RNASEQ {
         )
         multiqc_report = MULTIQC.out.report.toList()
     }
->>>>>>> origin/dev
 }
 
 /*
@@ -842,14 +821,12 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report, fail_percent_mapped)
     }
-<<<<<<< HEAD
-    NfcoreTemplate.summary(workflow, params, log)
+
     if (params.hook_url) {
         NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
     }
-=======
+
     NfcoreTemplate.summary(workflow, params, log, fail_percent_mapped, pass_percent_mapped)
->>>>>>> origin/dev
 }
 
 /*